Dataset Information

Proteotoxic stress response in in-vitro 2 human neuronal models 3

ABSTRACT: We used an untargeted pro-24 teomic approach using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify 25 and characterize time-series proteome-wide changes in dose-responsive mild and extreme proteo-26 toxic stress models in medulloblastoma [Daoy], neuroblastoma [SH-SY5Y] and differentiated SH-27 SY5Y neuronal cells. Combined global analysis of condition-time point datasets identified 1010 dif-28 ferentially expressed proteins (DEPs) in Daoy cells, 623 in SH-SY5Y cells, and 365 in differentiated 29 SH-SY5Y cells. The condition-specific analysis presents more DEPs and upregulated proteins in ex-30 treme heat stress with a relatively conservative and tight regulation in differentiated SH-SY5Y neu-31 ronal cells. Functional network analysis using ingenuity pathway analysis (IPA) identified path-32 ways associated with biological processes of protein, RNA, and amino acid metabolism, cellular 33 response to stress, and membrane trafficking as common to the three cell types.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Stem Cell, Cell Culture

DISEASE(S): Cardiovascular System Disease

SUBMITTER: Ayodele Alaiya

LAB HEAD: Dr_Ayodele Alaiya

PROVIDER: PXD051826 | Pride | 2025-08-25

REPOSITORIES: Pride

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			Action	DRS
	DSH-SC10H-08062023-01.raw.zip	Raw
	DSH-SC16H-08062023-02.raw.zip	Raw
	DSH-SC20H-08062023-01.raw.zip	Raw
	DSH-SC26H-08062023-01.raw.zip	Raw
	DSH-SC2C-08062023-02.raw.zip	Raw

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Publications

Proteomics Analysis of Proteotoxic Stress Response in In-Vitro Human Neuronal Models.

Alaiya Ayodele A Alharbi Bothina Mohammed BM Shinwari Zakia Z Rashid Mamoon M Albinhassan Tahani H TH Bouchama Abderrezak A Alwesmi Mai B MB Mohammad Sameer S Malik Shuja Shafi SS

International journal of molecular sciences 20240620 12

Heat stroke, a hazardous hyperthermia-related illness, is characterized by CNS injury, particularly long-lasting brain damage. A root cause for hyperthermic neurological damage is heat-induced proteotoxic stress through protein aggregation, a known causative agent of neurological disorders. Stress magnitude and enduring persistence are highly correlated with hyperthermia-associated neurological damage. We used an untargeted proteomic approach using liquid chromatography-tandem mass spectrometry ...[more]

PMID: 38928492

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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. 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.