Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression Profiling of Adult Male Germ Cell Tumors

ABSTRACT: Expression profiling of a panel of 101 adult male germ cell tumors and 5 normal testis specimens was performed on Affymetrix U133A and U133B microarrays. This data has been used to: 1) generate a gene classifier that predicts histology (see PMID 15870693). 2) identify candidate target genes on 12p, a region that is gained in almost 100% of germ cell tumors (see PMID 16424014) 3) identify pluripotency associated genes through comparison of pluripotent embryonal carcinoma vs. undifferentiated seminoma. ONGOING: 4) Identification of genes associated with patient outcome and cisplatin resistance. Keywords: germ cell tumor, histologic subtypes

ORGANISM(S): Homo sapiens

PROVIDER: GSE3218 | GEO | 2005/11/10

SECONDARY ACCESSION(S): PRJNA92737

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcription profiling of human adult male germ cell tumours

Project description:Expression profiling of a panel of 101 adult male germ cell tumors and 5 normal testis specimens was performed on Affymetrix U133A and U133B microarrays. This data has been used to:; 1) generate a gene classifier that predicts histology (see PMID 15870693). 2) identify candidate target genes on 12p, a region that is gained in almost 100% of germ cell tumors (see PMID 16424014); 3) identify pluripotency associated genes through comparison of pluripotent embryonal carcinoma vs. undifferentiated seminoma. ONGOING:; 4) Identification of genes associated with patient outcome and cisplatin resistance. Experiment Overall Design: Tumor tissues were collected under IRB-approved protocols at the Memorial Sloan-Kettering Cancer Center, New York, between 1987 and 1999. The tumor samples consist of 17 seminomas, 15 pure EC, 15 pure T, 10 pure YS, 2 pure CC, and 42 NSGCT with mixed histologies. There were six patients who had each had two tumors per patient that were included in this study (designated with the same number but different letter- e.g. 155A and 155C are from same patient but represent two different tumors, one being the primary testicular lesion, the other being a liver metastasis). Five normal testis specimens (and one pooled sample consisting of equal amounts of the 5 normal testis specimens) from individual of similar ages were used as controls.

2008-06-12 | E-GEOD-3218 | biostudies-arrayexpress

Transcriptional and epigenetic changes from the genesis of the human male germline through to adulthood provide a map of prenatal and postnatal molecular drivers of differentiation and reveal the developmental origin of seminoma.

Project description:Aberrancies in male germline development can lead to the formation of seminoma, a testicular germ cell tumor. Seminomas are biologically similar to primordial germ cells (PGCs) and many bear an isochromosome 12p [i(12p)] with two additional copies of the short arm of chromosome 12. By mapping of seminoma transcriptomes and open chromatin landscape onto our normal human male germline trajectory, we find that seminoma resembles premigratory/migratory primordial germ cells, but exhibit enhanced germline and pluripotency programs and upregulate genes involved in apoptosis, angiogenesis, and MAPK/ERK pathways. By modeling seminoma using pluripotent stem cell-derived primordial germ cells from Pallister Killian syndrome patients mosaic for i(12p), we identify gene dosage effects that may contribute to transformation. As murine seminoma models do not exist, our analyses provide insights into genetic, cellular and signaling programs driving seminoma transformation and our in vitro platform will permit future evaluation of additional signals required for seminoma tumorigenesis.

2024-07-10 | GSE256162 | GEO

Transcription profiling of human cisplatin based chemotherarpy adult male germ cell tumor patients - validation set for prediction of outcome

Project description:This series represents expression profiles of 34 non-seminoma germ cell tumors (NSGCTs) from patients who received cisplatin based chemotherarpy for treatment of their disease for whom full clinical follow-up information was available. These specimens were used as a validation set to test outcome prediction models using a subset of previously profiled GCT specimens (see GEO accession #GSE3218). Experiment Overall Design: Tumor tissues were collected under IRB-approved protocols at the Memorial Sloan-Kettering Cancer Center, New York, between 1987 and 2003. The tumor samples consist of 34 NSGCT specimens. RNA was isolated, labeled, and hybridized to Affymetrix U133A and U133B microarrays using standard protocols. Data were processed by the RMA method.

2008-10-26 | E-GEOD-10783 | biostudies-arrayexpress

Proteome characterization of germ cell tumor-related somatic-type malignancies for the identification of tissue origin, cisplatin resistance mechanisms, and putative therapeutic options

Project description:Germ cell tumors (GCT) can be distinguished into seminoma and non-seminoma. The latter comprises embryonal carcinoma, which can further differentiate into choriocarcinoma, teratoma (TER), and yolk-sac tumors (YST). However, GCT can transform into a somatic-type malignancy (STM), eventually resulting in an unfavorable outcome. This study aimed at enlightening the molecular mechanisms leading to STM formation by comparing them to TER and YST as presumable tissues of origin, thereby paving the way for the identification of novel druggable targets.

2024-01-26 | PXD039546 | Pride

Identification of potential biomarkers in testicular cancer by SILAC and mass spectrometry

Project description:This study represents a proteomic resource for testis cancer with quantitative protein expression data for 5236 proteins. By quantitative mass-spectrometry-based proteomics, we compared the two Malignant germ cell tumour cell lines, TCam-2 with seminoma-like characteristics, and NTERA-2, an embryonal carcinoma-like cell line.

2019-11-12 | PXD010275 | Pride

Genomic Screening of Testicular Germ Cell Tumors from Monozygotic Twins

Project description:Genomic screening was performed for one family containing MZ twins with testicular germ cell tumors, in order to define alterations associated with risk of tumor development. Copy number alterations were evaluated using array-CGH (4x44K, Agilent Technologies) in one seminoma and one embryonal carcinoma (EC) from MZ twins. In addition, genomic alterations from the tumors and peripheral blood cells of the twins were compared to the parental genomes via their peripheral blood cells.

2015-01-31 | E-GEOD-62779 | biostudies-arrayexpress

Identification of factors secreted by testicular germ cell tumor cell lines and microenvironmental cells.

Project description:Type II germ cell tumors (GCTs) are the most common neoplasia in young men of age 14-45 years. It is generally accepted that GCTs arise from a common precursor lesion, called germ cell neoplasia in situ (GCNIS), eventually developing into seminomas or non-seminomas, such as (embryonal carcinomas, ECs). The latter stem-cell like EC can further differentiate into teratomas (TE), yolk-sac tumors (YST), or choriocarcinomas (CC). Even though cisplatin-based chemotherapy is an efficacious standard of care during the management of GCT patients, the development of cisplatin resistance remains a major obstacle. As such, the surrounding tumor microenvironment and its secreted factors could endorse the development of drug resistance. These stromal cells, including immune cells (e.g. macrophages, T-lymphocytes), endothelial cells, and fibroblasts, can influence tumor cells by promoting proliferative and anti-apoptotic signaling pathways. Vice versa, microenvironmental cells can be influenced by tumor cells as well. For the identification of secreted proteins, cell lysates and supernatants from seven human germ cell tumor cell lines (seminoma: TCam-2; embryonal carcinoma (EC): 2102EP, NCCIT; choriocarcinoma (CC): JAR, JEG-3), yolk-sac tumor (YST): GCT72; 1411H) and five human cell types from the microenvironment (fibroblasts: MPAF, HVHF2; M2 macrophages: THP-1-M2; T-lymphocytes: JURKAT; endothelial cells: HUVEC) have been evaluated using liquid chromatography coupled with mass spectrometry (LC-MS).

2022-10-13 | PXD031329 | Pride

Effect of facioscapulohumeral dystrophy (FSHD) on skeletal muscle gene expression

Project description:Muscle biopsies taken from vastus lateralis muscle of 30 normal subjects and 19 FSHD subjects (see PubMed ID 17151338) Affymetrix U133A and U133B arrays were scanned both before (S1) and after (S2) antibody enhancement. Effects of age and sex in normal subjects reported previously under GSE362, GSE674, and GSE9676. Keywords: facioscapulohumeral dystrophy, skeletal muscle

2008-03-08 | GSE10760 | GEO

Genome-wide expression microarray analysis of SOX2-deficient TCam-2 cells in vivo

Project description:Illumina expression microarray analysis of seminoma-like TCam-2 cells depleted for SOX2 by CRISPR/Cas9. Cells were xenografted in nude mice. 2120EP embryonal carcinoma and parental TCam-2 cells were xenograted as controls. Tumors were recovered after 1 (1w) and 6 weeks (clone 1 - 5) of in vivo growth. Additionally, in vitro cultivated TCam-2 were analyzed as control. The data set is part of the study 'SOX2 is essential for in vivo reprogramming of seminoma-like TCam-2 cells to an embryonal carcinoma-like fate' (Nettersheim et al., 2016, Oncotarget).

2016-05-22 | GSE79065 | GEO

Validation Set for Prediction of Outcome in Adult Male Germ Cell Tumors

2008-09-30 | GSE10783 | GEO