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PROVIDER: PRJNA102729 | ENA |
REPOSITORIES: ENA
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Project description:Background: SH-SY5Y cells exhibit a neuronal phenotype when treated with all-trans retinoic acid (RA), but the molecular mechanism of activation in the signaling pathway mediated by phosphatidylinositol 3-kinase (PI3K) is not sufficiently understood. To shed new light on the mechanism, we comprehensively compared the gene expression profiles between SK-N-SH cells and two subtypes of SH-SY5Y cells (SH-SY5Y-A and SH-SY5Y-E), each of which showed a different phenotype during RA-mediated differentiation. Results: SH-SY5Y-A cells differentiated in the presence of RA, whereas RA-treated SH-SY5Y-E cells required additional treatment with brain-derived neurotrophic factor (BDNF) for full differentiation. In combination with perturbation using a PI3K inhibitor, LY294002, we identified 386 genes and categorized them into two clusters dependent on the PI3K signaling pathway during RA-mediated differentiation in SH-SY5Y-A cells. Transcriptional regulation of the gene cluster was greatly reduced in SK-N-SH cells or partially impaired in SH-SY5Y-E cells in coincidence with a defect in the neuronal phenotype of these cell lines. Additional stimulation with BDNF induced a set of neural genes which were down-regulated in RA-treated SH-SY5Y-E cells but were abundant in the differentiated SH-SY5Y-A cells. Conclusions: We identified the gene clusters controlled by PI3K- and TRKB-mediated signaling pathways during differentiation in two subtypes of SH-SY5Y cells. TRKB-mediated bypass pathway compensates for the impaired neural functions generated by defects in several signaling pathways including PI3K in SH-SY5Y-E cells. The expression profiling data are useful for further studies to elucidate the signal transduction-transcriptional network including PI3K and/or TRKB. Keywords: Cell type comparison, time course
2009-09-01 | GSE9169 | GEO
Project description:Background: SH-SY5Y cells exhibit a neuronal phenotype when treated with all-trans retinoic acid (RA), but the molecular mechanism of activation in the signaling pathway mediated by phosphatidylinositol 3-kinase (PI3K) is not sufficiently understood. To shed new light on the mechanism, we comprehensively compared the gene expression profiles between SK-N-SH cells and two subtypes of SH-SY5Y cells (SH-SY5Y-A and SH-SY5Y-E), each of which showed a different phenotype during RA-mediated differentiation. Results: SH-SY5Y-A cells differentiated in the presence of RA, whereas RA-treated SH-SY5Y-E cells required additional treatment with brain-derived neurotrophic factor (BDNF) for full differentiation. In combination with perturbation using a PI3K inhibitor, LY294002, we identified 386 genes and categorized them into two clusters dependent on the PI3K signaling pathway during RA-mediated differentiation in SH-SY5Y-A cells. Transcriptional regulation of the gene cluster was greatly reduced in SK-N-SH cells or partially impaired in SH-SY5Y-E cells in coincidence with a defect in the neuronal phenotype of these cell lines. Additional stimulation with BDNF induced a set of neural genes which were down-regulated in RA-treated SH-SY5Y-E cells but were abundant in the differentiated SH-SY5Y-A cells. Conclusions: We identified the gene clusters controlled by PI3K- and TRKB-mediated signaling pathways during differentiation in two subtypes of SH-SY5Y cells. TRKB-mediated bypass pathway compensates for the impaired neural functions generated by defects in several signaling pathways including PI3K in SH-SY5Y-E cells. The expression profiling data are useful for further studies to elucidate the signal transduction-transcriptional network including PI3K and/or TRKB. Experiment Overall Design: Human neuroblastomas, SK-N-SH (HTB-11) and SH-SY5Y-A cells (CRL-2266) were obtained from the American Type Culture Collection (ATCC). We also obtained SH-SY5Y-E cells (EC94030304) from the European Collection of Cell Cultures (ECACC). Tissue culture cells were maintained in D-MEM/F12 1:1 mixture supplemented with 15% FBS (Fetal Bovine Serum) and 1% NEAA (Non-essential amino acid) in a 5% CO2 humidified incubator at 37oC. The culture medium was changed twice a week. For the RA-inducible experiment, random culture cells from two clone subtypes of SH-SY5Y and SK-N-SH were seeded in laminin coated culture dishes (BioCoat Laminin Cellware; BD Biosciences, Billerica, MA, USA) for 1 day and then transferred to a medium containing 10 μM of RA in the presence or the absence of LY294002 (10μM) for five days. For BDNF-induced sequential differentiation of the SH-SY5Y-E strain, cells were washed with D-MEM/F12 twice after five days in the presence of RA and then incubated with 50 ng/ml of BDNF in D-MEM/F12 without serum for three days.
2009-09-04 | E-GEOD-9169 | biostudies-arrayexpress
Project description:Gene expression profile during SH-SY5Y neuroblastoma differentiation
| PRJNA248790 | ENA
Project description:The human neuroblastoma cell lines SH-SY5Y and IMR-32 can be differentiated into neuron-like phenotypes through treatment with all-trans retinoic acid (ATRA). After differentiation, these cell lines are extensively utilized as in vitro models to study various aspects of neuronal cell biology. However, temporal and quantitative profiling of the proteome and phosphoproteome of SH-SY5Y and IMR-32 cells throughout ATRA-induced differentiation has been limited. Here, we performed relative quantification of the phosphoproteomes of SH-SY5Y and IMR-32 cells at multiple time points during ATRA-induced differentiation. The data presented serve as a valuable resource for investigating temporal protein and phosphoprotein abundance changes in SH-SY5Y and IMR-32 cells during ATRA-induced differentiation.
2024-01-24 | PXD046871 | Pride
Project description:The human neuroblastoma cell lines SH-SY5Y and IMR-32 can be differentiated into neuron-like phenotypes through treatment with all-trans retinoic acid (ATRA). After differentiation, these cell lines are extensively utilized as in vitro models to study various aspects of neuronal cell biology. However, temporal and quantitative profiling of the proteome and phosphoproteome of SH-SY5Y and IMR-32 cells throughout ATRA-induced differentiation has been limited. Here, we performed relative quantification of the proteomes of SH-SY5Y and IMR-32 cells at multiple time points during ATRA-induced differentiation. The data presented serve as a valuable resource for investigating temporal protein and phosphoprotein abundance changes in SH-SY5Y and IMR-32 cells during ATRA-induced differentiation.
2024-01-24 | PXD046900 | Pride
Project description:MicroRNA-664a-5p promotes neuronal differentiation of SH-SY5Y cells
| PRJNA369739 | ENA
Project description:SH-SY5Y neuroblastoma cells are widely used as in vitro neuronal model. They can be induced to a differentiated phenotype, presenting neurites and synaptical-like structures in response to retinoic (RA) acid and brain-derived neurotrophic factor (BDNF), providing a model to analyze neuronal differentiation. We report a large scale MS quantification of SH-SY5Y cells proteome during its differentiation process after treatment with RA/BDNF. Using isobaric tags for relative and absolute quantification (iTRAQ) approach and phosphopeptide enrichment protocols, we identified a total of 5587 proteins, 366 of them showed differential abundance between both conditions of culture. Differentiated SH-SY5Y cells showed regulation of proteins and phosphosites strongly related to neuronal development, in contrast, undifferentiated cells expressed proteins more related to cell proliferation and control of cell cycle. Interactive network analysis covered processes as focal adhesion, cytoskeleton dynamics and neurodegenerative diseases and pathway analysis displayed regulation of mitogen-activated protein kinase and phosphoinositide 3-kinase/Akt signaling pathways mainly; the proteins involved in those processes might be considered as markers for neuronal differentiation. Overall the data collection presented here can be explored for any studies which intent to use SH-SY5Y as neuronal model.
| MSV000080133 | MassIVE
Project description:Neuroblastoma cells SH-SY5Y undergoes a morphology change upon retinoic acid (RA) treatment, the neurite outgrowth characteristic in undividing cells is accompanied by cell cycle arrest and neuronal markers expression, controlled by a precise dynamic molecular circuits. Depletion of CSB in SH-SY5Y cells leads to differentiation defects. This study examines the temporal gene expression profile during differentiation. Using Nimblegen microarray we characterized the gene expression profiles before and after RA treatment in both wild type and CSB-KD SH-SY5Y cells, and we identified the difference in gene expression between wild type and CSB-KD cells underlying the differentiation defects induced by CSB depletion.
2014-09-22 | GSE58070 | GEO
Project description:MicroRNAs (miRNAs) belong to a class of small non-coding RNAs that play important roles in the transcriptional regulation of gene expression. A number of miRNAs are known to act as key regulator of diverse processes such as neuronal differentiation. In this study, we have attempted to identify novel miRNAs related to neuronal differentiation. 15 upregulated and 8 downregulated miRNAs were identified in SH-SY5Y cells treated with all-trans retinoic acid. We further showed that one of the upregulated miRNAs, miR-664a-5p promoted neuronal differentiation of SH-SY5Y cells. Herein, we report for first time the important role of miR-664a-5p in SH-SY5Y cells.
2017-02-13 | GSE94447 | GEO
Project description:To reveal the molecular mechanism underling necrotic neuronal cell death caused by norephedrine, we examined alteration of gene expression profile during norephedrine exposure in human neuroblastoma SH-SY5Y cells. The alteration of gene expression during norephedrine exposure (3 mM, 0,2 and 6 hours) in differentiated SH-SY5Y cells was examined.
2015-04-08 | E-GEOD-67643 | biostudies-arrayexpress