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Epigenome analysis of parental (native) and 3-bromopyruvate-resistant UM-UC-3 bladder cancer cells

ABSTRACT: Epigenome analysis of parental (native) and 3-bromopyruvate-resistant UM-UC-3 bladder cancer cells

PROVIDER: PRJNA726980 | ENA |

REPOSITORIES: ENA

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Epigenome analysis of parental (native) and 3-bromopyruvate-resistant UM-UC-3 bladder cancer cells

Project description:Genome-wide DNA methylation profiling of parental (native) and 3-bromopyruvate-resistant UM-UC-3 bladder cancer cells. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in treatment-naive and 3-bromopyruvate-resistant UM-UC-3 bladder cancer cells.

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Effect of AR isoform and total AR depletion and AR-v19 oeverexpression in UM-UC-3 bladder cancer cells

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Project description:To better understand the molecular mechanisms underlying TYRO3 oncogenic activity in bladder carcinomas, we made use of MGH-U3, RT112 and UM-UC-5 cell lines, which were derived from a human bladder tumor and endogenously expressed the Tyro3 protein, the growth and transformation of these cell lines being dependent on Tyro3. We carried out a gene expression analysis using Affymetrix DNA arrays in this cell line treated or not withTYRO3 siRNAs.

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Project description:When applying deconvolution methods to bulk RNAseq data, a limitation of most prior studies is the lack of paired scRNA-seq and bulk RNA-seq data from the same samples to serve as ground truth for deconvolution. Our UC cohort, containing matched scRNA-seq and bulk RNA-seq data therefore provided a unique opportunity. (The scRNAseq datasets have been published before [PMID: 32111252 PMID: 36129800 PMID: 36099881 PMID: 33837006 ]. Please see linked manuscript for details) We assembled a scRNA-seq dataset of 100,667 cells from 30 UC tissue samples (20 unique patients). Bulk RNA sequencing was performed on a subset of patients(14) in the single-cell RNA sequencing cohort due to tissue availability.

2024-01-01 | GSE223971 | GEO

Effect of AR isoform and total AR depletion and AR-v19 oeverexpression in UM-UC-3 bladder cancer cells

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Project description:UC Raw sequence reads

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lncRNA and mRNA Expression Profiling in Early Stage UM CLL

Project description:Predicting disease progression in chronic lymphocytic leukemia (CLL) remains challenging particularly in patients with Rai Stage 0/I disease that have an unmutated immunoglobulin heavy chain variable region (UM IGHV). Even though patients with UM IGHV have a poor prognosis and generally require earlier treatment, not all UM IGHV patients experience more rapid disease progression with some remaining treatment free for many years. This observation suggests biologic characteristics other than known prognostic factors influence disease progression. Alterations in long non-coding RNA (lncRNA) expression levels have been implicated in diagnosis and prognosis of various cancers, however, their role in disease progression of early Rai stage UM CLL is unknown. Here we use microarray analysis to compare lncRNA and mRNA profiles of Rai 0/I UM IGHV patients who progressed in <2 years relative to patients who had not progressed for >5 years. Over 1300 lncRNAs and 940 mRNAs were differentially expressed (fold change ≥ 2.0; p-value ≤ 0.05). Of interest, the differentially expressed lncRNAs G047155, TCAM1P, and uc.436, have known associated genes that have been linked to CLL. Thus, our study reveals differentially expressed lncRNAs in progressive early stage CLL requiring therapy versus indolent early Rai stage UM CLL. These lncRNAs have the potential to impact relevant biological processes and pathways that influence clinical outcome in CLL.

2018-11-29 | GSE123075 | GEO

Expression profile of lncRNAs in CSCs and non-CSCs of bladder cancer cell line

Project description:Bladder cancer stem cells (CSCs) contribute to tumorigenesis, recurrence and chemoresistance of bladder cancer. However, the molecular mechanisms underlying their self-renewal are poorly unknown. Long noncoding RNAs (lncRNAs) act as crucial regulators in a lot of human cancers, yet their potential roles and molecular mechanisms in bladder CSCs are poorly understood. The goal of this study is to identify the differentially expressed lncRNAs in bladder CSCs (UM-UC-3 4th spheres), its two differentiation sublines and bladder non-CSCs (UM-UC-3). Our study reveals that deregulation of lncRNAs is involved in the bladder CSCs.

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