Bladder tumor sequencing
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE81201 | GEO | 2016/12/31
SECONDARY ACCESSION(S): PRJNA320879
REPOSITORIES: GEO
Similar Datasets
Project description:Tumor-associated blood vessels differ from normal vessels at the morphological and molecular level. Proteins that are only present on tumor vessels may serve as biomarkers and as therapeutic targets for inhibition of angiogenesis in cancer. Comparing the transcriptional profiles of blood vascular endothelium from human invasive bladder cancer and from normal bladder tissue, we found several markers that could serve as novel biomarkers or therapeutic targets. In this dataset, we include the expression data obtained from laser capture microdissected (LCM) vessels isolated from tumor and bladder normal tissue. 10 samples were analyzed. We compared expression of tumor associated blood vessels with expression of vessels in the normal bladder tissue using Genespring GX 12.
2013-03-08 | E-GEOD-41614 | biostudies-arrayexpress
Project description:In this study, we aimed to seek out abnormal noncoding RNAs (lncRNAs and circRNAs) involved in the development of bladder cancer through RNA-seq analysis. Transcriptome analysis of five pairs of bladder cancer tumor tissues and matched adjacent non-tumor tissues was completed in this project. A total of 68.18Gb clean data (sequencing data after quality control) was obtained. In conclusion, high-throughput sequencing analysis provided a distinctive landscape for the expression of noncoding RNAs and screened a series of significantly differently expressed lncRNAs and circRNAs, such as lncRNA LNPPS (ENST00000622374) and circSLC38A1. Further studies will focus on the potential function and intrinsic regulatory mechanisms of these significantly differently expressed lncRNAs and circRNAs in the development of bladder cancer.
2023-01-04 | GSE190079 | GEO
Project description:Tumor-associated blood vessels differ from normal vessels at the morphological and molecular level. Proteins that are only present on tumor vessels may serve as biomarkers and as therapeutic targets for inhibition of angiogenesis in cancer. Comparing the transcriptional profiles of blood vascular endothelium from human invasive bladder cancer and from normal bladder tissue, we found several markers that could serve as novel biomarkers or therapeutic targets. In this dataset, we include the expression data obtained from laser capture microdissected (LCM) vessels isolated from tumor and bladder normal tissue.
2013-03-08 | GSE41614 | GEO
Project description:Responses to anti-PD-1 immunotherapy occur but are infrequent in bladder cancer. The specific T cells that mediate tumor rejection are unknown. T cells from human bladder tumors and non-malignant tissue were assessed with single-cell RNA and paired T cell receptor (TCR) sequencing of 30,604 T cells from 7 patients. We find that the states and repertoire of CD8+ T cells are not altered in tumors compared with non-malignant tissues. In contrast, single-cell analysis of CD4+ T cells demonstrates several tumor-specific states, including multiple distinct states of regulatory T cells. Surprisingly, we also find multiple cytotoxic CD4+ T cell states that are clonally expanded. These CD4+ T cells can kill autologous tumor in an MHC class II-dependent fashion and are suppressed by regulatory T cells. Further, a gene signature of cytotoxic CD4+ T cells in tumors predicts a clinical response in 244 metastatic bladder cancer patients treated with anti-PD-L1.
2020-06-01 | GSE149652 | GEO
Project description:Investigating intra-tumor heterogeneity of bladder cancer has been largely based on conventional pathological staging and bulk samples sequencing for analyzed multiple spatially separated regions within one tumor. However, it still lack a comprehensive understanding for this question at single cell resolution.
2021-11-11 | GSE135337 | GEO
Project description:As no one previously examined urine-derived cells from bladder cancer patients, we performed scRNAseq to profile the diversity of these cells and their transcriptional profiles. We used scRNAseq to compare the profiles of urine-derived cells to matched tumor cells and PBMC from bladder cancer patients.
2024-05-17 | GSE267718 | GEO
Project description:Bladder cancer is the fifth most prevalent cancer in the U.S., yet is understudied and relatively lacking in suitable models. Here we describe a biobank of patient-derived organoid lines that recapitulates the spectrum of human bladder cancer at the histopathological and molecular levels. Organoid lines can be established efficiently from patient biopsies, including from patients before and after disease recurrence, and are interconvertible with orthotopic xenografts. Notably, these organoid lines often retain tumor heterogeneity and exhibit changes in their mutational profiles that are consistent with tumor evolution in culture. Analyses of drug response using bladder tumor organoids show partial correlations with mutational profiles as well as changes associated with treatment resistance, and specific responses can be validated using xenografts in vivo. Overall, our studies indicate that patient-derived bladder tumor organoids represent a model system for studying tumor evolution and treatment response in the context of precision cancer medicine.
2018-04-09 | GSE103990 | GEO
Project description:The general aim is to provide knowledge of transcriptomic profiles of the developing urinary bladder in order to shed light on gene expression important in the mechanisms behind the developmental defects of bladder exstrophy. Human bladder tissues and gential tissues, as control samples, were surgically removed from terminated fetuses after informed consent and ethical approval. Gene expression data were extracted and analysed after high throughput sequencing of paired-end mRNA libraries (Illumina).
2019-01-01 | E-MTAB-6592 | biostudies-arrayexpress
Project description:The aims of this study were to determine the impact of different levels of RNA degradation as well as to ascertain if the gene expression profiles obtained from bladder washing correlates to that obtained from the related bladder tumor. Keywords: RNA degradation, bladder washing, bladder tumor, bladder cancer
2005-08-25 | GSE3192 | GEO
Project description:This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines including information on origin, mutation status of genes implicated in bladder cancer (FGFR3, PIK3CA, TP53, and RAS), copy number alterations assessed using high density SNP arrays, uniparental disomy (UPD) events, and gene expression. Based on gene mutation patterns and genomic changes we identify lines representative of the FGFR3-driven tumor pathway and of the TP53/RB tumor suppressor-driven pathway. High-density array copy number analysis identified significant focal gains (1q32, 5p13.1-12, 7q11, and 7q33) and losses (i.e. 6p22.1) in regions altered in tumors but not previously described as affected in bladder cell lines. We also identify new evidence for frequent regions of UPD, often coinciding with regions reported to be lost in tumors. Previously undescribed chromosome X losses found in UBC lines also point to potential tumor suppressor genes. Cell lines representative of the FGFR3-driven pathway showed a lower number of UPD events. Overall, there is a predominance of more aggressive tumor subtypes among the cell lines. We provide a cell line classification that establishes their relatedness to the major molecularly-defined bladder tumor subtypes. The compiled information should serve as a useful reference to the bladder cancer research community and should help to select cell lines appropriate for the functional analysis of bladder cancer genes, for example those being identified through massive parallel sequencing. Expression levels were assessed in 20 bladder cell lines, included in the UBC-40 Urothelial Bladder Cell Line Index, with Affymetrix U133 array platform
2015-06-19 | E-GEOD-64279 | biostudies-arrayexpress