Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA137239 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The aim of this study was to compare effect of everolimus on growth of different renal cell carcinoma (RCC) populations and develop design for experiments to measure the early response of everolimus in clear cell RCC (ccRCC) cell lines including renal cancer stem cells. Gene expression profiling using microarray was performed to determine the early response to everolimus after 3 days of treatment with optimizied concentration of drug in two ccRCC cell lines 1) parental clear cell renal cell carcinoma ccRCC-PCSC (HKPCSC -human parental kidney cancer stem cells) and 2) ccRCC-CSC - clear cell renal cell carcinoma -cancer stem cells (HKCSC - human kidney cancer stem cells).
2018-05-31 | GSE106819 | GEO
Project description:Uncovering a protein abundance-based gene panel specific to clear cell Renal Cell Carcinoma (ccRCC) could provide support for the everyday clinical decision-making process. We used proteomic data to differentiate between normal kidney and ccRCC tissues. By using datasets of patients with paired normal tissue samples from gene array cohorts, we uncovered the top genes over-expressed in ccRCC. We collected surgically resected ccRCC specimens at Semmelweis University to validate the strongest genes. Differential expression was evaluated at the protein level using targeted mass spectrometry (MS).
2023-05-10 | PXD033709 | Pride
Project description:Despite numerous studies reporting deregulated microRNA (miRNA) and gene expression patterns in clear cell renal cell carcinoma (ccRCC), no direct comparisons have been made to its presumed normal counterpart; the renal proximal epithelial tubular cells (PTEC). The aim of this study was to determine the miRNA expression profiles of ten clear cell renal cell carcinoma-derived cell lines and short-term cultures of PTEC, and to correlate these with their gene expression, and copy-number profiles. Using microarray-based methods, a significantly altered expression level in ccRCC cell lines was observed for 23 miRNAs and 1630 genes. The set of miRNAs with significantly decreased expression levels include all members of the miR-200 family known to be involved in the epithelial to mesenchymal transition (EMT) process. Expression levels of 13 of the 47 validated target genes for the downregulated miRNAs were increased more than two-fold. Our data reinforce the importance of the EMT process in the development of ccRCC. For mRNA expression data of these cell lines see GEO Series accession number GSE20491. MicroRNA profiling was performed on two proximal tubular epithelial cell samples (both cell samples were hybridized twice (biological duplicates)) and ten clear cell renal cell carcinoma- derived cell lines (one of which; RCC-JF in duplicate)
2012-11-01 | E-GEOD-34981 | biostudies-arrayexpress
Project description:Aberrant DNA methylation is common in cancer. To associate DNA methylation with gene function, we performed RNAseq upon tumor tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients. To quantify 5mC and 5hmC level in each CG site at genome-wide level, we performed BS-seq and TAB-seq upon tumor tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients, respectively. mRNA profiles of tumor and matched normal tissues from two ccRCC patients were generated by deep sequencing, using Hiseq 2000. Single-nucleotide-resolution, whole-genome, 5mC and 5hmC profiles of tumor and matched normal tissues from two ccRCC (clear cell renal cell carcinoma) patients were generated by deep sequencing, using Hiseq 2000.
2016-02-29 | E-GEOD-63183 | biostudies-arrayexpress
Project description:Clear-cell renal cell carcinoma (ccRCC) is one of the most common urological malignant neoplasms. In addition, ccRCC is a highly aggressive cancer with a concomitant poor prognosis. Forkhead box K2 (FOXK2) has been reported to involve in many molecular mechanisms.However, little is known about the role FOXK2 plays in clear-cell renal cell carcinoma. Our previous study showed that FOXK2 mRNA and protein expression were decreased in human ccRCC tissues and suppressed the proliferation of ccRCC cells both in vitro and in vivo. We used microarrays (Affymetrix HTA2.0 Array) to detail the differentially expressed genes after overexpression of FOXK2, and aim to find potential one or more target gene/genes of FOXK2
2016-12-23 | GSE92777 | GEO
Project description:While early stages of clear cell renal cell carcinoma (ccRCC) are curable, survival outcome for metastatic ccRCC remains poor. The purpose of the current study was to apply a new individualized bioinformatics analysis (IBA) strategy to these transcriptome data in conjunction with Gene Set Enrichment Analysis of the Connectivity Map (C-MAP) database to identify and reposition FDA-approved drugs for anti-cancer therapy. We demonstrated that one of the drugs predicted to revert the RCC gene signature towards normal kidney, pentamidine, is effective against RCC cells in culture and in a RCC xenograft model. Most importantly, pentamidine slows tumor growth in the 786-O human ccRCC xenograft mouse model. To determine which genes are regulated by pentamidine in a human RCC cell line, 786-O, we treated these cells with pentamidine and performed transcriptional profiling analysis. We used microarrays to determine the set of genes regulated by pentamidine in 786-O renal cell cancer cells. Total RNA was isolated from 786-O cells treated with 25 μM pentamidine or vehicle control (DMSO) for 6 hours and hybridized to Affymetrix microarrays.
2014-08-05 | E-GEOD-54709 | biostudies-arrayexpress
Project description:The proteome of clinical tissue samples diagnosed with clear cell renal cell carcinoma (ccRCC) and papillary renal cell carcinoma (pRCC) were evaluated analyzed along with the dataset identifier PXD022018 to establish a potential discriminative biomarker panel of proteins for these tumors subtypes.
2021-12-15 | PXD023296 | Pride
Project description:MicroRNAs (miRNAs), non-coding RNAs regulating gene expression, are frequently aberrantly expressed in human cancers. Next-generation deep sequencing technology enables genome-wide expression profiling of known miRNAs and discovery of novel miRNAs at unprecedented quantitative and qualitative accuracy. Deep sequencing was performed on 22 fresh frozen clear cell renal cell carcinoma (ccRCC), 11 non-tumoral renal cortex (NRC) samples and 2 ccRCC cell lines (n=35). The 22 ccRCCs patients belonged to 3 prognostic sub-groups, i.e. Those without disease recurrence, with recurrence and with metastatic disease at diagnosis Deep sequencing was performed on 22 fresh frozen clear cell renal cell carcinoma (ccRCC), 11 non-tumoral renal cortex (NRC) samples and 2 ccRCC cell lines (n=35). The 22 ccRCCs patients belonged to 3 prognostic sub-groups, i.e. Those without disease recurrence, with recurrence and with metastatic disease at diagnosis.
2012-06-21 | E-GEOD-37616 | biostudies-arrayexpress
Project description:Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a workflow integrating different -omics technologies to identify ccRCC-specific HLA-presented peptides as potential drug targets for ccRCC immunotherapy. We analyzed frequent ccRCC-specific peptides by MS-based HLA ligandomics of 55 ccRCC tumors (cohort 1), paired non-tumor renal tissues and 158 benign tissues from other organs. Pathways enriched in ccRCC compared to its cell type of origin were identified by transcriptome and gene set enrichment analyses in 51 tumor tissues of the same cohort. To retrieve a list of candidate target genes with involvement in ccRCC pathogenesis, ccRCC-specific pathway genes were intersected with the source genes of tumor-exclusive peptides. The candidates were validated in an independent cohort from the Cancer Genome Atlas (TCGA KIRC, n=452), yielding 113 candidate genes. DNA methylation (TCGA KIRC, n=273), and somatic mutations (TCGA KIRC, n=392), as well as correlations with tumor metabolites (cohort 1, n=30) and immune-oncological markers (cohort 1, n=37) were analyzed to refine regulatory and functional involvements of candidates. Immunogenicity analysis identified candidate epitopes able to activate native CD8+ T cells. Functional analysis of EGLN3, a candidate with frequent ccRCC-specific immunogenic peptides, revealed possible tumor-promoting functions. Integration of HLA ligandomics, transcriptomics, genetic and epigenetic data leads to the identification of novel functionally relevant therapeutic targets for ccRCC immunotherapy. Validation of the identified targets is now mandatory to expand the treatment landscape of ccRCC.
2020-04-03 | PXD017149 | Pride
Project description:Set domain-containing 2 (SETD2) is the most frequently mutated gene among all the histone methyltransferases (HMTs) in Clear cell renal cell carcinoma (ccRCC). Loss of function of SETD2 is significantly associated with poor prognosis in patients with ccRCC. A better understanding of the roles of SETD2 played in ccRCC can greatly improve the prognosis and quality of life of patients with kidney cancer. Clear cell renal carcinoma cell A498 were treated with si-SETD2 and si-NC, and the exosomes were extracted.
2021-12-31 | GSE155810 | GEO