Expression data from human immortalized urothelial cell SV-HUC-1 and four Bladder cancer cells (5637, UMUC3, T24, and J82)
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE231383 | GEO | 2024/04/28
REPOSITORIES: GEO
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Project description:We profile gene expression upon circCDYL KD in HepG2 cells and in two bladder cancer cell lines J82 and UMUC3 as well as upon knockdown of the RNA binding proteins (RBP) GRWD1, IGF2BP1, and IGF2BP2 in J82 and UMUC3
2020-11-11 | GSE146726 | GEO
Project description:We profile gene expression upon circHIPK3 KD in two bladder cancer cell lines UMUC3 and J82
2021-10-01 | GSE148824 | GEO
Project description:Urine is an ideal material to study and examine the bladder cancer (BCa) biomarkers, whereas exploration to the corresponding protein candidates is confronting technique challenges. Herein, we proposed a comprehensive strategy of searching the urine proteins related to BCa. The strategy consists of three core combinations, screening the candidates in the secreted proteins derived from the BCa cell lines and verifying them in the patient urines, defining the differential proteins through two-dimensional electrophoresis (2DE) and isobaric tags for relative and absolute quantitation (iTRAQ), and implementing quantitative analysis in profiling and targeting proteomics. The differential proteins were globally and quantitatively determined between the two typical cell lines of BCa, T24 and 5637, and the immortalized normal uroepithelium cell line, SV-HUC-1, while the BCa related proteins were verified between the relatively normal and patient urines. With proteomic survey combined with 2DE and iTRAQ, a total of 724 secreted proteins were identified as the BCa related proteins. With label-free quantitative proteomics, the 96 candidates were detected in the pooled urine samples. Furthermore, the multiple reaction monitoring (MRM)-based quantification was adapted to verify these urine proteins in individual urines that were collected from 23 BCa patients and 24 relative normal people, and resulted in the 10 urine proteins with significant abundance differences between the two groups. Of the potential indicators for BCa, analysis of receiver operating characteristics (ROC) revealed the combination of complement component 3 (CO3) and lactose dehydrogenase B (LDHB) was more sensitive and efficient to distinguish healthy and disease urine. The discovery of the indicative proteins of BCa through our strategy has thus paved an avenue to further validation of BCa biomarkers in urine.
2016-06-17 | PXD003557 | Pride
Project description:RNA-Seq of circHIPK3 knockdown (KD) samples in UMUC3 and J82
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Project description:Several reports showed that SQLE was upregulated in some types of cancer, and it is essential for cancer development. Herein, to uncover the role of SQLE in BCa, we performed the RNA-seq to detect the gene expression levels in BCa cell line J82 with overexpression of SQLE.
2024-04-28 | GSE231045 | 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:RNA-Seq of circCDYL knockdown (KD) samples in HepG2, J82, and UMUC3 cells and of GRWD1, IGF2BP1, and IGF2BP2 knockdown (KD) samples in J82 and UMUC3 cells
| PRJNA611768 | ENA
Project description:J82 is a urothelial carcinoma (bladder cancer) derived cultured cell line (see COSMIC https://cancer.sanger.ac.uk/cosmic/sample/overview?id=753566). The cultured cell line MDXC1 was derived from J82 xenograft tumors grown in SCID/BEIGE mice for 50 days using conventional methods of tumor excision, cell dissociation and growth in culture for 15 passages. MDXC1 was confirmed to be solely of human origin and pathogen-free. J82 and MDXC1 cells were compared for phenotypic changes in cancer-related genes associated with xenograft tumor growth. Experiments were included in the following larger study: Title: Autocrine signaling by receptor tyrosine kinases in urothelial carcinoma of the bladder. Authors: Young H. Lee, Molly M. Lee, Dinuka M. De Silva, Arpita Roy, Cara Wright, Tiffany Wong, Rene Costello, Oluwole Olaku, Robert L. Grubb III#, Piyush K. Agarwal, Andrea B. Apolo*+ Donald P. Bottaro* Affiliations: Urologic Oncology Branch and +Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 USA and #Department of Urology, Medical University of South Carolina, Charleston, South Carolina 29425 USA Abstract: Comprehensive characterizations of bladder cancer (BCa) have established molecular phenotype classes with distinct alterations and survival trends. Extending these studies within the tyrosine kinase (TK) family to identify disease drivers could improve our use of TK inhibitors to treat specific patient groups or individuals. We examined the expression distribution of TKs as a class (n = 89) in The Cancer Genome Atlas (TCGA) muscle invasive BCa data set (n >400). Patient profiles of potentially oncogenic alterations (overexpression and/or amplification) clustered TKs into 3 groups; alterations of group 1 and 3 TKs were associated with significantly worse patient survival relative to those without alterations. Many TK pathways induce epithelial-to-mesenchymal transition (EMT), which promotes tumor invasiveness and metastasis. Overexpression and/or amplification among 9 EMT transcriptional activators occurred in 43% of TCGA cases. Co-occurring alterations of TKs and EMT transcriptional activators involved most group 1 TKs; 24% of these events were associated with significantly worse patient survival. Co-occurring alterations of receptor TKs and their cognate ligands occurred in 16% of TCGA cases and several BCa-derived cell lines. Suppression of GAS6, MST1 or CSF1, or their respective receptors (AXL, MST1R and CSF1R), in BCa cell lines was associated with decreased receptor activation, cell migration, cell proliferation and anchorage independent cell growth. These studies reveal the patterns and prevalence of potentially oncogenic TK pathway-related alterations in BCa and identify specific alterations associated with reduced BCa patient survival. Detection of these features in BCa patients could better inform TK inhibitor use and improve clinical outcomes.
2021-07-28 | GSE156348 | GEO
Project description:Urine is an ideal material to study and examine the bladder cancer (BCa) biomarkers, whereas exploration to the corresponding protein candidates is confronting technique challenges. Herein, we proposed a comprehensive strategy of searching the urine proteins related to BCa. The strategy consists of three core combinations, screening the candidates in the secreted proteins derived from the BCa cell lines and verifying them in the patient urines, defining the differential proteins through two-dimensional electrophoresis (2DE) and isobaric tags for relative and absolute quantitation (iTRAQ), and implementing quantitative analysis in profiling and targeting proteomics. The differential proteins were globally and quantitatively determined between the two typical cell lines of BCa, T24 and 5637, and the immortalized normal uroepithelium cell line, SV-HUC-1, while the BCa related proteins were verified between the relatively normal and patient urines. With proteomic survey combined with 2DE and iTRAQ, a total of 724 secreted proteins were identified as the BCa related proteins. With label-free quantitative proteomics, the 96 candidates were detected in the pooled urine samples. Furthermore, the multiple reaction monitoring (MRM)-based quantification was adapted to verify these urine proteins in individual urines that were collected from 23 BCa patients and 24 relative normal people, and resulted in the 10 urine proteins with significant abundance differences between the two groups. Of the potential indicators for BCa, analysis of receiver operating characteristics (ROC) revealed the combination of complement component 3 (CO3) and lactose dehydrogenase B (LDHB) was more sensitive and efficient to distinguish healthy and disease urine. The discovery of the indicative proteins of BCa through our strategy has thus paved an avenue to further validation of BCa biomarkers in urine.
2017-03-28 | MSV000080696 | MassIVE
Project description:Frankincense oil is prepared from aromatic hardened wood resin obtained by tapping Boswellia trees. For thousands of years, it has been important both socially and economically as an ingredient in incense and perfumes. Frankincense oil is a botanical oil distillate made from fermented plants that contains boswellic acid, a component known to have anti-neoplastic properties. We evaluated frankincense oil-induced cytotoxicity in bladder cancer cells. With a window of concentration, frankincense oil suppressed cell viability and induced cytotoxicity in bladder transitional carcinoma J82 cells but not normal bladder urothelial UROtsa cells immortalized with SV40 large T antigen. However, frankincense oil-induced J82 cell death did not result in DNA fragmentation. Microarray and bioinformatics analysis confirmed that frankincense oil activated cell cycle arrest, suppressed cell proliferation, and activated apoptosis in J82 cells through a series of potential pathways. These finding suggest that bladder cancer can be treated through intravesical administration of pharmaceutical agents similar to direct application on melanoma. 2E05 J82 cells were untreated or treated with a 1/1000 dilution of frankincense oil for 0.5, 1, 2, or 3 hours prior to RNA extraction.
2009-02-09 | E-GEOD-14002 | biostudies-arrayexpress