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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression Profiling of Clear cell renal carcinoma

ABSTRACT: 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).

ORGANISM(S): Homo sapiens

SUBMITTER: Elarouci Nabila

PROVIDER: E-MTAB-3267 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Molecular subtypes of clear cell renal cell carcinoma are associated with sunitinib response in the metastatic setting.

Beuselinck Benoit B Job Sylvie S Becht Etienne E Karadimou Alexandra A Verkarre Virginie V Couchy Gabrielle G Giraldo Nicolas N Rioux-Leclercq Nathalie N Molinié Vincent V Sibony Mathilde M Elaidi Reza R Teghom Corinne C Patard Jean-Jacques JJ Méjean Arnaud A Fridman Wolf Herman WH Sautès-Fridman Catherine C de Reyniès Aurélien A Oudard Stéphane S Zucman-Rossi Jessica J

Clinical cancer research : an official journal of the American Association for Cancer Research 20150112 6

<h4>Purpose</h4>Selecting patients with metastatic clear-cell renal cell carcinoma (m-ccRCC) who might benefit from treatment with targeted tyrosine kinase inhibitors (TKI) is a challenge. Our aim was to identify molecular markers associated with outcome in patients with m-ccRCC treated with sunitinib.<h4>Experimental design</h4>We performed global transcriptome analyses on 53 primary resected ccRCC tumors from patients who developed metastatic disease and were treated with first-line sunitinib. ...[more]

PMID: 25583177

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Genotyping by array of 108 clear cell renal cell carcinoma

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net); 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.

2015-01-27 | E-MTAB-3269 | biostudies-arrayexpress

Methylation profiling by array of 108 clear cell renal cell carcinoma

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the French Ligue Nationale Contre le Cancer (<a href=\\ttp://cit.ligue-cancer.net/\\ target=\\_blank\\>http://cit.ligue-cancer.net</a>). 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.\

2016-02-26 | E-MTAB-3274 | biostudies-arrayexpress

Impact of sunitinib resistance on clear cell renal cell carcinoma therapeutic sensitivity in vitro

Project description:Sunitinib resistance creates a major clinical challenge for the treatment of advanced clear cell renal cell carcinoma (ccRCC) and functional and metabolic changes linked to sunitinib resistance are not fully understood. We sought to characterize the molecular and metabolic changes induced by the development of sunitinib resistance in ccRCC by developing and characterizing the transcriptome of two human ccRCC cell lines resistant to sunitinib.

2024-04-17 | GSE216494 | GEO

Control of oxidative stress by miRNA and impact on ovarian tumorigenesis

Project description:Transcriptome analysis of high-grade human ovarian adenocarcinomas. The hypothesis tested in the present study was that two reciprocal pathways, namely oxidative stress response and fibrosis, enable to build a hierarchical cluster of ovarian patients. Ovarian human tumor samples from Institut Curie were analysed on human genome U133 plus 2.0 array (Affymetrix). Microarray analysis was performed using Partek Genomic Suite software and transcriptomic data were normalized using GCRMA algorithm. Probes from oxidative stress response and fibrosis defined by Ingenuity software were used to build a hierarchical cluster of ovarian patients.

2011-11-01 | E-GEOD-26193 | biostudies-arrayexpress

Expression profile of non-muscle invasive (superficial) bladder carcinoma

Project description:Gene expression profiling of 82 human non-muscle invasive bladder carcinoma and 4 normal bladder samples, for a total of 86 tissues. A Cartes d‚àö‚â†Identite des Tumeurs (CIT) study from the 'Institut Curie' and the french 'Ligue Nationale Contre le Cancer' (http://cit.ligue-cancer.net/).

2015-01-01 | E-MTAB-1940 | biostudies-arrayexpress

Gene expression changes during resistance toward vascular endothelial growth factor receptor (VEGFR) tyrosine kinase inhibitor (TKI) therapy in renal cell carcinoma (RCC)

Project description:This study was performed to understand the gene expression changes that accompany treatment of renal cell carcinoma (RCC) with vascular endothelial growth factor receptor (VEGFR) tyrosine kinase inhibitor (TKI) therapy. Human RCC cell lines were implanted into the flanks of nude beige mice, allowed to reach 12mm in long axis, and then treated with TKIs (sunitinib or sorafenib). Tumors were excised at 2 timepoints (prior to any therapy and at the 20mm endpoint of the study) and gene expression analysis was performed. Sunitinb or sorafenib were administered to mice bearing either 786-O or A498 xenografts. Mice were sacrificed and tumors excised for RNA extraction at pretreatment size of 12mm, or at 20mm, the mandated maximum tumor size allowed at our institution.

2015-05-21 | E-GEOD-64052 | biostudies-arrayexpress

Major Action of Endogenous Lysyl Oxidase in Clear Cell Renal Cell Carcinoma Progression and Collagen Stiffness Revealed by Primary Cell Cultures

Project description:In this work we aimed to perform, for the first time in human clear cell renal cell carcinoma (ccRCC), a comprehensive and detailed study of endogenous LOX expression and functions. To overcome the difficulties and limitations due to tissue heterogeneity, we took advantage of a consolidated in vitro model of primary cell cultures that we obtained from normal kidney and ccRCC tissues. We have previously extensively characterized these primary cell cultures for their proteomic, cellular, and genomic features, and we also investigated here for their transcriptomic profile by using Affymetrix technology. This in vitro model has been instrumental for the molecular and functional analysis of endogenous LOX related to ccRCC progression.

2016-06-06 | E-MTAB-4074 | biostudies-arrayexpress

Expression data from pulmonary metastases and primary tumors of clear-cell renal cell carcinoma (ccRCC) with different disease-free survivals

Project description:The understanding of metastatic spread is limited and molecular mechanisms causing particular characteristics of metastasis are largely unknown. This comprises the extremely varying dormancy periods of tumor cells in the secondary organ after metastatic spread, represented by the disease-free survival (DFS) of the patients, or differing numbers of metastases in different patients. Knowing the molecular fundamentals of these phenomena would support the individual prediction of patientsÂ´ outcome and facilitate the decision for an appropriate monitoring and therapy regime. In a first study (PMID 19391132) we analyzed the transcriptome-wide expression profiles of 20 pulmonary metastases of renal cell carcinoma (Met1-9, Met11-18, Met20, Met23, Met25) to identify expression patterns associated with the dormancy period and the number of metastases per patient. Pre-processed and analyzed data for this study are available in GEO Series GSE14378. In this second study, we validated the DFS-associated expression pattern from the first study on four further metastases and also included primary ccRCC with different DFS. For this, the microarray data of all metastases and primary tumors were pre-processed together. The aim of this second study was to identify those genes, which are differentially expressed in metastases developed after different dormancy periods and which are already deregulated in primary tumors. Genes differentially expressed in synchronously vs. metachronously metastases might contribute functionally to the dormancy period. Genes already deregulated in primary ccRCC might be suitable for prognostic purposes. metastases manifested synchronously or metachronously (DFS less than or equal to 9 months compared with DFS greater than or equal to 60 months); primary ccRCC which developed synchronous or metachronous metastases (DFS less than or equal to 6 months compared with DFS greater than or equal to 45 months)

2010-07-30 | E-GEOD-22541 | biostudies-arrayexpress

microRNAseq of clear-cell renal cell carcinoma on surgical resection specimens of untreated primary tumors in humans

Project description:We aimed to assess differences in miRNA expression profiles in transcriptomic molecular subtypes of ccRCC (Beuselinck et al, Clinical Cancer Research 2015) and to correlate miRNAs with overal survival since diagnosis of ccRCC. Sequencing was done for 129 primary ccRCC (formalin-fixed paraffin-embedded surgical resection specimens, previously untreated) and 16 normal kidney specimens. Normal kidney was obtained from the nephrectomy specimens at time of ccRCC removal, in tissue blocks containing only normal kidney (so nót the normal kidney immediately adjacent to ccRCC). The samples were sequenced in 2 major batches (2014 and 2017).

2020-07-22 | E-MTAB-9380 | biostudies-arrayexpress

miRNA array of clear cell renal cell carcinoma from patients treated with sunitinib

Project description:A multiple receptor tyrosine kinase inhibitor, sunitinib, is a first-line therapy for clear cell renal cell carcinoma (CCRCC). Unfortunately, it has the major challenges of low initial response rate and resistance after about one year of treatment. Here we evaluated a microRNA (miRNA) and its target responsible for sunitinib resistance. Using miRNA profiling, we identified miR-96-5p upregulation in tumors from sunitinib-resistant CCRCC patients

2021-12-03 | GSE189331 | GEO

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