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Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer

ABSTRACT: Urothelial carcinoma of the bladder is characterized by significant variability in clinical outcomes depending on stage and grade. The addition of molecular information may improve our understanding of such heterogeneity and enhance prognostic prediction. The purpose of this study was to validate and improve published prognostic signatures for high-risk bladder cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE31684 | GEO | 2012/01/23

SECONDARY ACCESSION(S): PRJNA145647

REPOSITORIES: GEO

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Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer Â

Project description:Urothelial carcinoma of the bladder is characterized by significant variability in clinical outcomes depending on stage and grade. The addition of molecular information may improve our understanding of such heterogeneity and enhance prognostic prediction. The purpose of this study was to validate and improve published prognostic signatures for high-risk bladder cancer. We evaluated microarray data from 93 bladder cancer patients managed by radical cystectomy to determine gene expression patterns associated with clinical and prognostic variables.

2012-01-23 | E-GEOD-31684 | biostudies-arrayexpress

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

Single cell transcriptomes of mouse bladder urothelium uncover novel cell type markers and urothelial differentiation characteristics.

Project description:Objectives: Much of the information to date in terms of subtypes and function of bladder urothelial cells were derived from anatomical location or by the expression of a small number of marker genes. To have a comprehensive map of the cellular anatomy of bladder urothelial cells, we performed single-cell RNA-sequencing to thoroughly characterize mouse bladder urothelium. Materials and methods: A total of 18,917 single cells from mouse bladder urothelium was analyzed by unbiased single-cell RNA sequencing. The expression of the novel cell marker was confirmed by immunofluorescence using urinary tract infections models. Results: Unsupervised clustering analysis identified 8 transcriptionally distinct cell subpopulations from mouse bladder urothelial cells. We discovered a novel type of bladder urothelial cells marked by Plxna4 that may be involved with host response and wound healing. We also found a group of basal-like cells labeled by ASPM that could be the progenitor cells of adult bladder urothelium. ASPM+ urothelial cells are significantly increased after injury by UPEC. In addition, specific transcription factors were found to be associated with urothelial cell differentiation. At the last, a number of interstitial cystitis/bladder pain syndrome-regulating genes were found differentially expressed among different urothelial cell subpopulations. Conclusions: Our study provides a comprehensive characterization of bladder urothelial cells, which is fundamental to understanding the biology of bladder urothelium and associated bladder disease.

2020-12-12 | GSE163029 | GEO

Expression profiling of Get1 -/- bladder

Project description:Skin and bladder epithelia form effective permeability barriers through the activation of distinct differentiation gene programs. Employing a genome-wide gene expression study, we identified transcription regulators whose expression correlates highly with that of differentiation markers both in bladder and skin, including the Grainyhead factor Get1/Grhl3, already known to be important for epidermal barrier formation. In the bladder, Get1 is most highly expressed in the differentiated umbrella cells and its mutation in mice leads to a defective bladder epithelial barrier formation due to failure of apical membrane specialization. Genes encoding components of the specialized urothelial membrane, the uroplakins, were downregulated in Get1-/- mice. At least one of these genes, Uroplakin II, is a direct target of Get1. The urothelial-specific activation of the Uroplakin II gene is due to selective binding of Get1 to the Uroplakin II promoter in urothelial cells, most likely regulated by histone modifications. These results demonstrate a key role for Get1 in urothelial differentiation and barrier formation.

2009-05-20 | GSE15768 | GEO

Transcriptomes of human bladder cells and cells in bladder cancer

Project description:Characterization of the gene expression profiles of specific cell populations of the human urinary bladder provides an important set of research tools for the study of cellular differentiation and the cancer process. The transcriptome is a definitive identifier of each individual cell types. Surgically resected tissue was digested by collagenase and the different cell types were sorted by antibodies to cluster designation (CD) cell surface antigens. The sorted cells were analyzed by DNA microarrays. The transcriptome datasets were analyzed for differentially expressed genes and plotted on a principal components analysis space for cell lineage relationship. The following bladder cell types were analyzed: CD9+ urothelial, CD104+ basal, CD13+ stromal of lamina propria, CD9+ urothelial carcinoma cancer, and CD13+ urothelial carcinoma-associated stromal. Gene expression differences between the cell types of tumor and their respective non-cancer counterpart provide biomarker candidates. Basal cells of the bladder and prostate, although sharing CD cell surface markers, are quite different in overall gene expression. Furthermore, these cells lack transcript features of stem cell signature of embryonic stem or embryonal carcinoma cells. Cell type-specific transcriptomes are more informative than bulk tissue transcriptomes. The relatedness of different cell types can be determined by transcriptome dataset comparison. Bladder cell types were sorted from tissue specimens, and analyzed by DNA microarrays. The various transcriptomes were compared by principal components analysis for cell lineage relationship.

2011-07-09 | E-GEOD-30522 | biostudies-arrayexpress

WT and Get1 +/- Bladder Time Course

2009-05-20 | GSE15770 | GEO

Frequent truncating mutations of STAG2 in bladder cancer

Project description:Here we report the discovery of truncating mutations of the gene encoding the cohesin subunit STAG2, which regulates sister chromatid cohesion and segregation, in 36% of papillary non-invasive urothelial carcinomas and 16% of invasive urothelial carcinomas of the bladder. Our studies suggest that STAG2 has a role in controlling chromosome number but not the proliferation of bladder cancer cells. These findings identify STAG2 as one of the most commonly mutated genes in bladder cancer. Affymetrix CytoScan HD Arrays were performed according to the manufacturer's directions on genomic DNA extracted directly from 12 snap-frozen human urothelial carcinoma primary tumors with somatic mutations of the STAG2 gene.

2013-06-30 | GSE41581 | GEO

Bladder tumour recurrence prediction

Project description:Expression profiling of superficial bladder tumours to delineate the expression pattern differences between non-recurring and recurring tumours. Keywords = bladder cancer, superficial, recurrence, prediction Keywords: other

2002-12-08 | GSE88 | GEO

Protein expression of bladder cancer

Project description:Expression profiling of a total of 656 proteins in 3 high grade non-muslce invasive bladder cancer cases/normal urothelial mucosa pairs

2014-07-16 | GSE59440 | GEO

Molecular Biomarker Signature for Bladder Cancer Detection

Project description:In this study we applied differential gene expression analysis to exfoliated human urothelia obtained from patients of known bladder disease status. Selected targets from the microarray data were validated in an independent set of samples using a quantitative PCR approach. Total RNA was extracted from 52 samples of human urothelial cancer cells (C) and from 40 samples of human non-cancer (NC) urothelial cells. Fragmented, biotinylated cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 microarrays.

2013-01-08 | E-GEOD-31189 | biostudies-arrayexpress

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