ABSTRACT: We used Affymetrix U133 plus 2.0 arrays to study the gene expression patterns of primaryBladder tumors (43 MIBC and 20 NMIBC) Total of 63 patients suffering from bladder cancer were included in our study, none of which received any prior therapy before surgery. Selected tumors belong to the CIT (“Carte d’Identité des Tumeurs”) discovery series.
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net: mRNA profiles were obtained using HumanGeneChip HG-U133 Plus 2.0 arrays (Affymetrix) for the 67 samples from the study (63 MPM tumors and 4 normal pleural samples). We used the RMA algorithm (Bioconductor affy package) to normalize the data. For each gene symbol, probe with the highest expression variance was kept.
Project description:A Cartes dM-^RIdentite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net/). Seven transcriptome datasets corresponding to a new series of 85 MIBC (Muscle-invasive bladder cancer) and six publicly-available series (298 MIBC) were analyzed. Tumors were classified by consensus clustering. Overall survival was determined from Kaplan-Meier curves. The role of the EGFR pathway was investigated by pathway bioinformatics analysis, determination of the expression levels of its components (by microarray, RT-qPCR and western blot) and of EGFR copy number by CGH arrays. A 40-gene transcriptomic classifier was used to identify basal-like cell lines and a basal-like mouse model. Please note M-^QMIBC molecular subtype': tumors classification using consensus clustering.
Project description:miRNAs are involved in cancer development and progression,acting as tumor suppressors or oncogenes. Half of the human miRNAs are located in cancer-associated genomic regions and can function as tumor suppressor genes or oncogenes depending on their targets miRNA profiling was performed on paired bladder cancer tissues and differentially expressed miRNAs were identified in BC and adjacent noncancerous tissues of any disease stage/grade. Ten paired bladder cancer tissues (5 low-grade non-muscle-invasive bladder cancer[NMIBC] and 5 high-grade muscle-invasive bladder cancer[MIBC]) were sent to CapitalBio Corp. (Beijing) for noncoding RNA microarray analysis. The microarray analysis was done as described on the Web site of CapitalBio. NMIBC samples include 07A, 19A, 23A, 24A and T63 while coresponding pairs include 07B, 19B, 23B, 24B and 63. MIBC samples include 10A, 20A, 21A, 34A and 49A while coresponding pairs include 10B, 20B, 21B, 34B and 49B.
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.
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net):we explored DNA methylation patterns associated with PPGL malignancy using two large and well characterized cohorts of PPGL collected through a multi-institutional collaboration through the European Network for the Study of Adrenal Tumors (ENS@T).
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 : 56 glioblastomas |Submitter : Aurelien de Reynies <reyniesa@ligue-cancer.fr> | Project leader : Francois Berger <fberger@ujf-grenoble.fr>
Project description:Clinical management of bladder carcinomas (BC) remains a major challenge and demands comprehensive multi-omics analysis for better stratification of the disease. Identification of patients on risk requires identification of signatures predicting prognosis risk of the patients. Understanding the molecular alterations associated with the disease onset and progression could improve the routinely used diagnostic and therapy procedures. In this study, we investigated the aberrant changes in N-glycosylation pattern of proteins associated with tumorigenesis as well as disease progression in bladder cancer. We integrated and compared global N-glycoproteomic and proteomic profile of urine samples from bladder cancer patients at different clinicopathological stages (non-muscle invasive and muscle-invasive patients (n=5 and 4 in each cohort)) with healthy subjects (n=5) using SPEG method. We identified 635 N-glycopeptides corresponding to 381 proteins and 543 N-glycopeptides corresponding to 326 proteins in NMIBC and MIBC patients respectively. Moreover, we identified altered glycosylation in 41 NMIBC and 21 MIBC proteins without any significant change in protein abundance levels. In concordance with the previously published bladder cancer cell line N-glycoproteomic data, we also observed dysregulated glycosylation in ECM related proteins. Further, we identified distinct N-glycosylation pattern of CD44, MGAM and GINM1 between NMIBC and MIBC patients, which may be associated with disease progression in bladder cancer. These aberrant protein glycosylation events would provide a novel approach for bladder carcinoma diagnosis and further define novel mechanisms of tumor initiation and progression.
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 : 5 mixed fibrolamellar carcinoma (m-FLC), 17 pure fibrolamellar carcinoma (p-FLC), 7 hepatocelluar carcinoma arising in non-cirrhotic liver (nc-HCC) and 10 non-tumoral livers (NL).
Project description:Because cystoscopy is expensive and invasive, a new method of detecting non-invasive muscular bladder cancer (NMIBC) is needed. This study aims to identify potential serum protein markers for NMIBC to improve diagnosis and to found treatment approaches to avoid disease progression to a life-threatening phenotype (muscle-invasive bladder cancer, MIBC). Here, silver nanoparticles (AgNPs, 9.73 ± 1.70 nm) as a scavenging device together with Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) were used to quantitative analyze the blood serum protein al-terations in two NMIBC subtypes: T1 and Ta, and they were compared to normal samples (HC). NMIBC's analysis of serum samples identified three major groups of proteins, the relative content of which is different from the HC content: proteins implicated in the complement and coagulation cascade pathways and apolipoproteins. In conclusion, many biomarker proteins were identified that merit further examination to validate their useful significance and utility within the clinical management of NMIBC patients.
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net); Integrative study based on 89 patients with Head and Neck Squamous Cell Carcinoma (HNSCC); 89 Affymetrix HG-U133 Plus 2.0 GeneChips arrays; 88 samples on HumanCNV370-Quad GeneChips arrays; 84 samples on Illumina Human Methylation 27K arrays;Micro-RNA sequencing of 64 tumors. Please note: Characteristics[MetastasisFreeSurvivalEvent] indicates if there is a metastasis-free survival for a particular sample / patient (it is like an event-free survival variable where the event considered is a metastasis). Characteristics[MetastasisFreeSurvivalDelay] - whenever the MetastasisFreeSurvivalEvent is 1, gives the duration of the metastasis-free survival period in months.