RNA-Seq analysis of bladder cancer cells after protodioscin treatment
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE212328 | GEO | 2024/08/30
REPOSITORIES: GEO
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Project description:The established cell lines RT4, 5637 and T24 from human bladder TCC were obtained from the Cell Bank of the Federal University of Rio de Janeiro, Brazil. The 5637 cells harbor two TP53 mutations, at codon 72 (Arg . Pro) and codon 280 (Arg . Thr).T24 cells contain a TP53 allele encoding an in-frame deletion of tyrosine 126. Both cell lines were established from high-grade bladder tumors. No specific mutations were detected in RT4 cells, which had been established from a low-grade papillary bladder tumor. The RT4 and T24 cell lines were maintained in DulbeccoM-^Rs modified EagleM-^Rs medium (Sigma-Aldrich, Inc, St Louis, MO, USA), and the 5637 cells were kept in Roswell Park Memorial Institute medium (Sigma-Aldrich). Both media were supplemented with 10% fetal bovine serum (Cultilab Ltd, Campinas, Brazil), 100 U/mL penicillin G (Sigma-Aldrich), 100 U/mL streptomycin (Sigma-Aldrich) and 1% kanamycin sulfate (Amresco, Branded Products Group, Solon, OH, USA); cells were cultured at 37M-:C in an atmosphere of 5% CO2. A pooled reference design was chosen. More specifically, each array was hybridized with the same reference sample labeled with Cy5, while the experimental samples (control or treated) were labeled with Cy3.
2010-10-30 | E-MEXP-2859 | biostudies-arrayexpress
Project description:Mitomycin C (MMC) is the gold standard treatment for non-muscle invasive bladder cancer (NMIBC). We aimed to evaluate in bladder cancer cell lines (T24, 5637, TCC-SUP and CLS-439) the transcriptomic response to MMC treatment. We used Gene Set Enrichment Analysis (GSEA) to identify biological processes and pathways modulated by MMC treatment.
2021-01-02 | GSE151505 | GEO
Project description:Bladder cancer, the most common malignancy of the urinary tract, has a poor overall survival rate if the tumor becomes muscle invasive. The discovery and evaluation of new alternative medications targeting high-grade muscle invasive bladder cancer (MIBC) are of tremendous importance in reducing bladder cancer mortality. Isorhapontigenin (ISO), a stilbene derivative from Chinese herb Gnetum cleistostachyum, exhibits a strong anti-cancer effect on MIBCs. Here, we report the whole transcriptome profiling of ISO-treated human bladder cancer T24 cells. A total of 1047 differentially expressed genes (DEGs) were identified, including 596 downregulated and 451 upregulated genes. Functional annotation and pathway analysis revealed that ISO treatment induced massive changes in gene expression associated with cell movement, migration, invasion, metabolism, proliferation, and angiogenesis. Additionally, ISO treatment activated genes involved in the inflammatory response but repressed genes involved in hypoxia signaling, glycolysis, the actin cytoskeleton, and the tumor microenvironment. In summary, our whole transcriptome analysis demonstrated a shifted metabolism and altered actin cytoskeleton in ISO treated T24 cells, which subsequently contribute to tumor microenvironment remodeling that suppresses tumor growth and progression.
2024-02-14 | GSE252406 | GEO
Project description:To uncover the dysregulated genes in BCa, we performed the RNA-seq to detect the gene expression levels in four BCa cells (5637, UMUC3, T24, and J82) and human immortalized urothelial cell SV-HUC-1. To search for the differentially expressed genes of for cell lines (5637, J82, UMUC3, and T24) compared to the normal cell line SV-HUC-1.
2024-04-28 | GSE231383 | GEO
Project description:We knocked down SOX4 in T24 cell and created 3 cell lines: T24-scrambled, T24-SOX4-knockdown and T24-SOX4-rescue and compared gene expression changes SOX4 is a developmental transcription factor that is overexpressed in as many as 23% of bladder cancer patients, but the role of SOX4 in bladder cancer tumorigenesis is not well understood. Given SOX4’s many roles in embryonic development and context-dependent regulation of gene expression, we sought to understand SOX4’s contribution to bladder cancer and to elucidate SOX4 regulated genes that might contribute to tumorigenesis. We employed a CRISPR interference (CRISPRi) method to transcriptionally repress SOX4 expression in T24 bladder cancer cell lines, rescued these cell lines with lentivirally expressed SOX4, and performed whole genome expression profiling. SOX4 knockdown cells exhibited decreased invasive capabilities but no changes in migration or proliferation, while rescue with SOX4 lentiviral vector restored the invasive phenotype. Gene expression profiling revealed 173 high confidence SOX4 regulated genes
2018-08-16 | GSE118572 | GEO
Project description:The aim of the present study was to identify novel DNA methylation markers in bladder cancer (BCa) through genome-wide profiling of bladder cancer cell lines and subsequent MSP screening in urine samples. Experimental Design: MBD methylCap/seq was carried out to screen differentially methylated CpG islands using two BCa cell lines (5637 and T24) and two normal bladder mucosa (BM) samples. The top one hundred most hypermethylated targets were screened using Methylation Specific PCR (MSP) in small and big cohort of urine samples from BCa patients and normal controls. The diagnostic performance of the gene panel was further evaluated in different clinical scenarios. Results: In total, 1,627 gene promoter regions hypermethylated in BCa cell line were identified in genomic level methylation profiling. The followed screening procedure in clinical urine sample generated eight genes (VAX1, KCNV1, ECEL1, TMEM26, TAL1, PROX1, SLC6A20, and LMX1A) capable of differentiating BCa from normal control. Subsequent validation in a large sample size enabled the optimisation of 5 methylation targets (VAX1, KCNV1, TAL1, PPOX1 and CFTR) for BCa diagnosis with sensitivity and specificity of 86.32% and 87.13%, respectively. In addition, VAX1 and LMX1A methylation could predict the tumour recurrence. Conclusions: Tumor specific biomarkers of BCa could be established by first performing genome level methylation profiling with cell lines and then screening the potential targets in urine samples. The panel of methylated genes identified was promising for the early non-invasive detection and surveillance of BCa. MBD methylCap/seq was carried out to screen differentially methylated CpG islands using two BCa cell lines (5637 and T24), and two normal bladder tissue mix as control.
2012-04-30 | E-GEOD-33839 | biostudies-arrayexpress
Project description:Bladder cancer (BC) is a major health concern retaining high mortality rates when diagnosed at advanced stages. In this context, the clinical management of BC requires the introduction of new biomarkers and molecular targets capable to elicit precision medicine therapeutical approaches. A promising candidate is cluster of differentiation 44 (CD44), a multifunctional and heavily glycosylated transmembrane protein, involved in cell-cell and cell-matrix adhesion, and a transducer of several oncogenic signalling cascades. CD44 has been widely explored as a marker of BC aggressiveness and cancer stem cells (CSC), but this is a highly heterogenic protein and the lack of molecular tools for precise molecular characterization has led to conflicting results, delaying clinical application. CD44 molecular variability results from the number of proteoforms arising from alternative splicing. The human CD44 gene consists of 17 exons, and while the exons 1-5 are constitutively expressed, exons 6-14 are subjected to alternative splicing, generating a myriad of different variants whose functional implications are yet to be fully understood. Furthermore, this number of proteoforms is greatly amplified by O-GalNAc glycosylation, which is predicted to mostly occur in the protein variable regions. This microheterogeneity and its relevance for BC can only be addressed by obtaining a comprehensive characterization at the protein level. Herein, we devised a strategy, combining transcriptomics, glycomics and mass spectrometry based proteomics data, to interrogate CD44 proteoform expression in a series of BC cell culture models showing different aggressiveness (5637 and T24) and a sample pool from formalin fixed paraffin embedded (FFPE) tumours. Glycoengeneered T24 cells expressing the Tn antigen (T24 C1GALT1 knockout (KO)) were also analysed.
2022-05-19 | PXD028307 | Pride
Project description:To identification of key drivers involved in the development of muscle invasive bladder cancer, which displays poor prognosis, we isolated one subpopulation of human 5637 bladder cancer cells with highly invasiveness and the other subpopulation of 5637 cells with low invasiveness by Transwell method. Through proteomic analysis, differentially expressed proteins were displayed.
2018-03-15 | PXD007709 | Pride
Project description:Study of the gene expression of T24 bladder cancer cells in response to hypericin-mediated photodynamic therapy in the absence or presence of the p38 MAPK inhibitor PD169316
2007-10-01 | E-MEXP-1220 | biostudies-arrayexpress
Project description:TCGA data analysis and clinical sample test results showed the IGF2BP3 is highly expressed in bladder cancer and related to tumor metastasis and invasion. RNA sequencing results of clinical bladder tissue from 53 cases showed that the IGF2BP3 expression is related to cell proliferation genes. M6a and RNA sequencing results showed the IGF2BP3 affects the growth, proliferation, and apoptosis of T24 cells, and SpHK1, POMT2, and MRPS18a may be potential targets of IGF2BP3.
2024-03-27 | GSE171023 | GEO