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Transcriptome profiling of TNFa-stimulated urothelial cells

ABSTRACT: In this study, we aimed to determine the overall effect of TNFα on transcriptomic profile of urothelial cells using RNA sequencing. Our study represents a reference database that could lead to a better understanding of the role of urothelial cells in IC/BPS pathology and more importantly, sets grounds for future studies exploring potential biomarkers and therapeutic targets for IC/PBS diagnosis and treatment.

ORGANISM(S): Homo sapiens

PROVIDER: GSE202576 | GEO | 2022/08/05

REPOSITORIES: GEO

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Transcription profiling by array of human female interstitial cystitis urothelial cells after inducing differentiation

Project description:Purpose: Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells. Materials and Methods: Bladder biopsies were taken from IC patients and controls (women having surgery for stress incontinence). Primary cultures were grown in Keratinocyte Growth Medium with supplements. To induce differentiation, in some plates the medium was changed to DMEM-F12 with supplements. RNA was analyzed with Affymetrix chips. Three nonulcer IC patients were compared with three controls. Results: After inducing differentiation, 302 genes with a described function were altered at least 3-fold with p <0.01 in both IC and control cells. Functions of the162 upregulated genes included cell adhesion (e.g. claudins, occludin, cingulin); urothelial differentiation, retinoic acid pathway and keratinocyte differentiation (e.g. skin cornified envelope components). The 140 downregulated genes included genes associated with basal urothelium (e.g. p63, integrins ?4, ?5 and ?6, basonuclin 1 and extracellular matrix components), vimentin, metallothioneins and members of the Wnt and Notch pathways. Comparing IC vs. control cells after differentiation, only seven genes with a described function were altered at least 3-fold with p <0.01. PI3, SERPINB4, CYP2C8, EFEMP2 and SEPP1 were decreased in IC; AKR1C2 and MKNK1 were increased in IC. Conclusions: Differentiation-associated changes occurred in both IC and control cells. Comparing IC vs. control revealed very few differences. This study may have included IC patients with minimal urothelial deficiency and/or selected the cells that were most robust in culture. Also, the abnormal urothelium in IC may be due to post-translational changes and/or the bladder environment. Experiment Overall Design: Human female urothelial cell cultures, differentiated vs. non-differentiated,interstitial cystitis vs. control

2008-10-25 | E-GEOD-11839 | biostudies-arrayexpress

Differentiation associated changes in gene expression profiles for interstitial cystitis and control urothelial cells

2008-09-05 | GSE11839 | GEO

Peptidomics analysis of urine from IC/BPS patients and healthy controls

Project description:Interstitial cystitis/bladder pain syndrome (IC/BPS) is a chronic and debilitating pain disorder of the bladder and urinary tract with poorly understood etiology. A definitive diagnosis of IC/BPS can be challenging because many symptoms of IC/BPS are shared with other urological disorders. An analysis of urine presents an attractive and non-invasive resource for monitoring and diagnosing IC/BPS. Here, a non-targeted LC-MS and LC-MS/MS-based peptidomics analysis of urine samples collected from IC/BPS patients were compared to urine samples from asymptomatic controls.

2022-06-06 | PXD031843 | Pride

Proteomic analyisis of cultured human podocytes stimulated with TNFa - supernatant

Project description:TNFa stimulated human cultured podocytes compared with unstimulated (vehicle control (VC)) podocytes. Incubation of podocytes with high concentrations of TNF alpha led to an overexpression of ICAM1 in particular. We studied this system as a comparator for organoids also stimulated with the same concentration of TNFa. Four conditions (6 replicates each) 1) treatment (5 ng/mL TNFa) for 24 hours 2) control (PBS) for 24h 3) treatment (5 ng/mL TNFa) for 48 hours 4) control (PBS) for 48h

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Elucidation of the mechanism of treatment by TGFβ inhibitors for the IC/PBS mouse model using hydrogen peroxide

Project description:Interstitial cystitis/painful bladder syndrome (IC/PBS) is a chronic disease for which there is no effective treatment.Transforming Growth Factor-β (TGF-β) is thought to be involved in the pathogenesis of IC/PBS, and previous studies have shown that suggested that administration of TGF-β inhibitors significantly ameliorates IC/PBS in a mouse model.However, the molecular mechanism of the therapeutic effect of TGF-β inhibitors on IC/PBS has not been comprehensively analyzed. In this study, we show that TGF-β inhibitor administration ameliorated dysuria in IC/PBS mouse models using hydrogen peroxide through a variety of mechanisms.

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Proteomic analyisis of cultured human podocytes stimulated with TNFa - cell pellet

2023-05-19 | PXD032107 | Pride

Chromatin Landscape of Normal Urothelial cells

Project description:Describing the chromatin landscape of normal urothelial cells by ChIPseq analysis of 6 histones marks and 1 chromatin factor in 2 patient derived Normal Human Urothelial cells

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Nanostring profiling of urothelial cells intracellularly infected with UPEC

Project description:The primary goals of this study are to: determine how intracellular infection of urothelial cells with uropathogenic Escherichia coli influences urothelial cell metabolism, and determine the influence of cytochrome bd on the urothelial cell response to infection

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Transcriptome analysis for KDM6A mutated urothelial bladder carcinoma and EZH2 inhibitor treated KDM6A mutated urothelial bladder carcinoma

Project description:Purpose: The goals of this study are to compare 1. The transcription profile in KDM6A wildtype and KDM6A mutated urothelial bladder carcinoma. 2. The transcriptional changes in KDM6A mutated urothelial bladder carcinoma upon EZH2 inhibitor treatment.

2017-03-01 | GSE92723 | GEO

In-depth protein profiling of cytology samples in urothelial carcinoma

Project description:Urine cytologic examination is a widely used primary pathologic screening test in the diagnosis of bladder urothelial carcinoma (BLCA), however the low diagnostic accuracy remains challenging. We conducted high-throughput proteome on ten pairs of BLCA and benign urothelial lesion (BUL) to identify a supportive proteomic marker as an ancillary test in liquid based cytology (LBC).

2018-07-04 | PXD006805 | Pride

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