Transcription profiling of human glioblastomas (56 tumor samples)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Aurelien de Reynies
PROVIDER: E-TABM-898 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:A Cartes dIdentite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | Affymetrix HG-U133 Plus 2.0 : 10 HSTL samples including biopsies (n=6), sorted tumor cells (n=3), cell line (n=1) | Agilent SurePrint G3 Human CGH Microarray 4x180K Arrays : 7 HSTL samples including biopsies (n=5), sorted tumor cells (n=1), cell line (n=1) | Submitter : Aurelien de Reynies <reyniesa@ligue-cancer.fr> | Project leader : Philippe Gaulard <philippe.gaulard@hmn.aphp.fr> The E-MTAB-638.additional.1.zip archive contains the CGH processed data file with additional chromosome coordiantes.
2011-09-30 | E-MTAB-638 | biostudies-arrayexpress
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | Affymetrix HG-U133 Plus 2.0 : 7 NKTCL biopsies, 2 NKTCL cell lines (SNK6, SNT8), 16 PTCL NOS biopsies, 2 NK cells samples | Biopsies and cell lines of NK/T-cell lymphoma, nasal-type (NKTCL) were subject to combined gene expression profiling and array-based comparative genomic hybridization analyses. Compared to PTCL, NOS, NKTCL had higher transcript levels for NK-cell markers and cytotoxic molecules, especially granzyme H, a novel sensitive biomarker of NKTCL. Compared to normal NK cells, tumors were closer to activated than resting cells and overexpressed several genes related to vascular biology, EBV-induced genes and PDGFRA. Notably, PDGFR? and its phosphorylated form were confirmed at the protein level, and in vitro the MEC04 NKTCL-cell line was sensitive to imatinib. Deregulation of the AKT, JAKSTAT and NF-?B pathways suggested by bioinformatical analysis, was corroborated by nuclear expression of phosphorylated AKT, STAT3 and RelA in NKTCL, and several deregulated genes in these pathways mapped to regions of recurrent copy number aberrations (AKT3 (1q44), IL6R (1q21.3), CCL2 (17q12), TNFRSF21 (6p12.3)). Several features of NKTCL uncovered by this analysis (overexpression of VEGFA and its receptor KDR by the tumor cells, overexpression of MET-HGF) suggest deregulation of angiogenic pathways. Integrative analysis also identified a novel putative tumor suppressor HACE1 in the frequently deleted 6q21 region. This study highlights emerging oncogenic pathways in NKTCL and identifies novel diagnostic and therapeutic targets. | Submitter : Aurelien de Reynies <reyniesa@ligue-cancer.fr> | Project leader : Philippe Gaulard <philippe.gaulard@hmn.aphp.fr>
2009-12-31 | E-TABM-702 | biostudies-arrayexpress
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net ) | Human genome-wide CIT-aCGH-V6-4.4K : 67 glioblastomas | Submitter : Aurelien de Reynies <reyniesa@ligue-cancer.fr> | Project leader : Francois Berger <fberger@ujf-grenoble.fr>
2010-06-30 | E-TABM-897 | biostudies-arrayexpress
Project description:A ï¾Cartes dï¾Identite des Tumeursï¾ (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net ) |Illumina 370K SNP chips (chromosome 11 subpart) : 80 HNSCC | Submitter : Aurelien de Reynies <reyniesa@ligue-cancer.fr> | Project leader : Bohdan Wazylyk <boh@igbmc.fr>
2010-05-15 | E-TABM-994 | biostudies-arrayexpress
Project description:A ﾑCartes dﾒIdentite des Tumeursﾒ (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net ) | Human genome-wide CIT-aCGH-V7-4.7K : 84 HNSCC | Submitter : Aurelien de Reynies <reyniesa@ligue-cancer.fr> | Project leader : Bohdan Wazylyk <boh@igbmc.fr>
2010-05-15 | E-TABM-995 | biostudies-arrayexpress
Project description:A ï¾Cartes dï¾Identite des Tumeursï¾ (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | Affymetrix HG-U133 Plus 2.0 : 17 AITL biopsies, 2 AITL sorted cells, 16 PTCL NOS biopsies | The molecular alterations underlying the pathogenesis of angioimmunoblastic T-cell lymphoma (AITL) and peripheral T-cell lymphoma, unspecified (PTCL-u) are largely unknown. In order to characterize the ontogeny and molecular differences between both entities, a series of AITLs (n = 18) and PTCLs-u (n = 16) was analyzed using gene expression profiling. Unsupervised clustering correlated with the pathological classification and with CD30 expression in PTCL-u. The molecular profile of AITLs was characterized by a strong microenvironment imprint (overexpression of B-cell- and follicular dendritic cell-related genes, chemokines, and genes related to extracellular matrix and vascular biology), and overexpression of several genes characteristic of normal follicular helper T (T(FH)) cells (CXCL13, BCL6, PDCD1, CD40L, NFATC1). By gene set enrichment analysis, the AITL molecular signature was significantly enriched in published T(FH)-specific genes. The enrichment was higher for sorted AITL cells than for tissue samples. Overexpression of several T(FH) genes was validated by immunohistochemistry in AITLs. A few cases with molecular T(FH)-like features were identified among CD30(-) PTCLs-u. Our findings strongly support that T(FH) cells represent the normal counterpart of AITL, and suggest that the AITL spectrum may be wider than suspected, as a subset of CD30(-) PTCLs-u may derive from or be related to AITL.| Submitter : Aurelien de Reynies <reyniesa@ligue-cancer.fr> | Project leader : Philippe Gaulard <philippe.gaulard@hmn.aphp.fr>
2009-09-22 | E-TABM-783 | biostudies-arrayexpress
Project description:A ï¾Cartes dï¾Identite des Tumeursï¾ (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net ) | Human genome-wide CIT-aCGH-V6-4.4K : 8 NKTCL biopsies, 2 NKTCL cell lines. Biopsies and cell lines of NK/T-cell lymphoma, nasal-type (NKTCL) were subject to combined gene expression profiling (see E-TABM-702) and array-based comparative genomic hybridization analyses. | Submitter : Aurelien de Reynies <reyniesa@ligue-cancer.fr> | Project leader : Philippe Gaulard <philippe.gaulard@hmn.aphp.fr>
2009-12-31 | E-TABM-791 | biostudies-arrayexpress
Project description:A Cartes d'Identité des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | Affymetrix HG-U133 Plus 2.0 : 46 samples| Agilent SurePrint G3 Human CGH Microarray 4x180K Arrays : 135 samples| To explore the prognostic value of genomic alterations present in primary tumours we perfom a comparative genomic hybridization study on BAC arrays for a panel of breast carcinoma from 45 patients with metastatic relapse and 95 others one, matched for age and axillary node involvement, without any recurrence after 11 years of follow up. Array CGH data was used in establishing a two parameters index representative first of the global level of aneusomy by chromosomal arm and second of the number of breackpoints throughout the genome. Submitter : Nabila Elarouci <elaroucin@ligue-cancer.fr> | Project leader : Michel Longy <longy@bergonie.org>
2012-02-01 | E-MTAB-748 | biostudies-arrayexpress
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the French National League Against Cancer (http://cit.ligue-cancer.net ) 25 glioblastoma multiforme tumors hybridized on Illumina SNP and Affymetrix gene expression arrays. Project leader : François DUCRAY (francois.ducray@chu-lyon.fr). CIT Analysis : Julien LAFFAIRE (laffairej@ligue-cancer.net). Note: PFS : progression-free survival, OS: Overall Survival,BCNU : Carmustine (chemotherapy agent). RESPONDER: if the patient has shown or not shown a response to the treatment (Bevacizumab (Avastin) plus Irinotecan). Progression during : If the disease has progressed (cancer relapse or patient's death); otherwise (patient is alive without relapse).
2013-01-15 | E-MTAB-951 | biostudies-arrayexpress
Project description:A ""Cartes d'Identite des Tumeurs"" (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net). 92 samples on Affymetrix HG-U133 Plus 2.0 GeneChips arrays for 92 patients with Adrenocortical Tumors (ACT). 4 normal adrenal samples from the same batch are also included. 10 ACTH-independant Macronodular Adrenal Hyperplasia (AIMAH) from the same batch are also included.
2009-01-15 | E-TABM-311 | biostudies-arrayexpress