RNAseq of clear cell renal cell carcinoma (ccRCC) tumor specimens
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB88258 | 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:Genome wide DNA methylation profiling of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in tumor and adjacent normal kidney tissue samples from ccRCC patients. Samples included 46 paired fresh frozen ccRCC tumor and adjacent normal kidney tissues. Bisulphite converted DNA from the 92 samples were hybridised to the Illumina Infinium 450 Human Methylation Beadchip v1.2
2015-10-26 | E-GEOD-61441 | biostudies-arrayexpress
Project description:To understand the tumor immune microenvironment (TIME), we sequenced CD45+ tumor infiltrating leukocytes (TILs) isolated from three primary and three lung metastatic clear cell renal cell carcinoma (ccRCC) specimens.
2024-12-06 | GSE267835 | GEO
Project description:Genome wide DNA methylation profiling of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in tumor and adjacent normal kidney tissue samples from ccRCC patients. Samples included 46 paired fresh frozen ccRCC tumor and adjacent normal kidney tissues.
2015-10-26 | GSE61441 | GEO
Project description:MBOAT7 loss of function in clear cell Renal Carcinoma (ccRCC)
| PRJNA545231 | ENA
Project description:Background: Clear cell renal cell carcinoma (ccRCC) and chromophobe renal cell carcinoma (chRCC) can usually be distinguished by histologic characteristics. Occasionally, diagnosis proves challenging and diagnostic difficulty will likely increase as needle biopsies of renal lesions become more common. Method: To identify markers that aid in differentiating ccRCC from chRCC, we used gene expression profiles to identify candidate markers that correlate with histology. 39 antisera and antibodies, including 35 for transcripts identified from gene expression profiling, were evaluated. Promising markers were tested on a tissue microarray (TMA) containing 428 renal neoplasms. Strength of staining of each core on the TMA was formally scored and the distribution of staining across different types of renal neoplasms was analyzed. Results: Based on results from initial immunohistochemical staining of multitissue titer arrays, 23 of the antisera and antibodies were selected for staining of the TMA. For 7 of these markers, strength of staining of each core on the TMA was formally scored. Vimentin (positive in ccRCC) and CD9 (positive in chRCC) best distinguished ccRCC from chRCC. The combination of vimentin negativity and CD9 positivity was found to distinguish chRCC from ccRCC with a sensitivity of 100.0% and a specificity of 95.2%. Conclusions: Based on gene expression analysis, we identify CD9 and vimentin as candidate markers for distinguishing between ccRCC and chRCC. In difficult cases and particularly when the amount of diagnostic tissue is limited, vimentin and CD9 staining could serve as a useful adjunct in the differential diagnosis of ccRCC and chRCC. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Disease State: Stage of Clear Cell renal cell carcinoma (I - V)) disease_state_design
2010-08-20 | E-GEOD-17746 | biostudies-arrayexpress
Project description:In order to clarify the molecular mechanism involved in renal carcinogenesis, and identify molecular targets for diagnosis and treatment, we analyzed genome-wide gene expression profiles of 15 surgical specimens of clear cell renal cell carcinoma (RCC), compared to normal renal cortex, using a combination of laser microbeam microdissection (LMM) with a cDNA microarray representing 27,648 genes. Tissue samples of surgically-resected clear cell renal cell carcinoma (ccRCC) and their corresponding clinical information were obtained from patients with written informed consent. The total of 15 cancer patients (6 women and 9 men; median age, 66; range, 36-75 years) that had been confirmed histologically as ccRCC were selected for this study. Two to three pieces of cancer tissue had been taken from each patient at the time of radical nephrectomy. Normal tissue had been obtained from the distant region from cancer area in the resected kidney tissue. These samples were immediately embedded in TissueTek OCT compound (Sakura, Tokyo, Japan), frozen, and stored at -80°C. The frozen tissues were sliced into 8-μm sections using a cryostat (Sakura) and then stained with H&E for histological examination. We used LMM technology to collect pure populations of ccRCC cells as well as non-cancerous renal cortex. A mixture of normal renal cortex cells in kidney tissues from 11 patients was prepared as a universal control. Experiments were performed using 6 sets of slides (slide set 1-6 corresponding to ID_REF 1-27648).
2012-07-15 | E-GEOD-39364 | biostudies-arrayexpress
Project description:Human clear cell renal cell carcinoma (ccRCC) is a common cancer of the kidney. We applied an integrated approach to identify important factors that influence carcinogenesis in ccRCC.
2011-12-01 | GSE27852 | GEO
Project description:Renal cell carcinoma (RCC) exhibits some unusual features and genes commonly mutated in cancer are rarely mutated in clear-cell RCC (ccRCC), the most common type. The most prevalent genetic alteration in ccRCC is the inactivation of the tumor suppressor gene VHL. Using whole-genome and exome sequencing we discovered BAP1 as a novel tumor suppressor in ccRCC that shows little overlap with mutations in PBRM1, another recent tumor suppressor. Whereas VHL was mutated in 81% of the patients (142/176), PBRM1 was lost in 58% and BAP1 in 15% of the patients analyzed. All these tumor suppressor genes are located in chromosome 3p, which is partially or completely lost in most ccRCC patients. However, BAP1 but not PBRM1 loss was associated with higher Fuhrman grade and, therefore, poorer outcome. Xenograft tumors (tumorgrafts) implanted orthotopically in mice retained >92% of mutations and exhibited similar DNA copy number alterations to corresponding primary tumors. Thus, after inactivation of VHL, the acquisition of a mutation in BAP1 or PBRM1 defines a different program that might alter the fate of the patient. Our results establish the foundation for an integrated pathological and molecular genetic classification of about 70% of ccRCC patients, paving the way for subtype-specific treatments exploiting genetic vulnerabilities. The genomic DNA of clear-cell renal cell carcinoma (ccRCC) primary tumors, tumors growing in immunodeficient mice (tumorgrafts), and normal samples were labeled and hybridized to Affymetrix SNP arrays 6.0.
2012-06-09 | E-GEOD-25540 | biostudies-arrayexpress
Project description:Selecting patients with metastatic clear-cell renal cell carcinoma (m-ccRCC) who might benefit from treatment with targeted tyrosine kinase inhibitors (TKIs) is a challenge. Our aim was to identify molecular markers associated with outcome in m-ccRCC patients treated with sunitinib. A Cartes d’Identite des Tumeurs (CIT) study from the 'Institut Curie' and the french 'Ligue Nationale Contre le Cancer' (http://cit.ligue-cancer.net).
2015-01-27 | E-MTAB-3267 | biostudies-arrayexpress