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ArrayCGH mapping of chromosome 3 aberrations in lung Squamous Cell Carcinoma (SCC)

ABSTRACT: To prospectively identify new oncogenes implicated in lung Squamous Cell Carcinoma pathogenesis, we investigated chromosome 3 aberrations in advanced tumours using arrayCGH. These aberrations are indeed among the most frequent aberrations in lung SCC and correlate with SCC patient's poor prognosis. We precisely map regions of recurrent losses at 3p and gains at 3q25-qter in a series of lung SCC. We moreover uncover 3q26.3-q27 high level amplifications in 20% of tumours. Keywords: ArrayCGH, Lung Squamous Cell Carcinoma, 3q26.3, SOX2 Profiling of 26 advanced (stage III) lung SCC. Replicates : each tumor sample is hybridized together with a normal dna sample to one microarray. Each microarray contain 3 replicates per BAC clone.

ORGANISM(S): Homo sapiens

SUBMITTER: Thomas Hussenet

PROVIDER: E-GEOD-14859 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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SOX2 is an oncogene activated by recurrent 3q26.3 amplifications in human lung squamous cell carcinomas.

Hussenet Thomas T Dali Soraya S Exinger Julien J Monga Ben B Jost Bernard B Dembelé Doulaye D Martinet Nadine N Thibault Christelle C Huelsken Joerg J Brambilla Elisabeth E du Manoir Stanislas S

PloS one 20100129 1

Squamous cell carcinoma (SCC) of the lung is a frequent and aggressive cancer type. Gene amplifications, a known activating mechanism of oncogenes, target the 3q26-qter region as one of the most frequently gained/amplified genomic sites in SCC of various types. Here, we used array comparative genomic hybridization to delineate the consensus region of 3q26.3 amplifications in lung SCC. Recurrent amplifications occur in 20% of lung SCC (136 tumors in total) and map to a core region of 2 Mb (Megaba ...[more]

PMID: 20126410

Similar Datasets

SOX2 is a new oncogene activated by the recurrent 3q26.3 amplifications in lung Squamous Cell Carcinoma

Project description:This SuperSeries is composed of the following subset Series: GSE14859: ArrayCGH mapping of chromosome 3 aberrations in lung Squamous Cell Carcinoma (SCC) GSE14883: SOX2 overexpression effect on human lung squamous cells GSE15079: ArrayCGH mapping of the recurrent 3q26.3-q27mplifications in lung Squamous Cell Carcinoma (SCC) Refer to individual Series

2010-05-14 | E-GEOD-15080 | biostudies-arrayexpress

ArrayCGH mapping of the recurrent 3q26.3-q27 amplifications in lung Squamous Cell Carcinoma (SCC)

Project description:To prospectively identify new oncogenes implicated in lung Squamous Cell Carcinoma pathogenesis, we investigated chromosome 3 aberrations in advanced tumours using arrayCGH. Chromosome 3 aberrations are indeed among the most frequent alterations in lung SCC and correlate with SCC patient's poor prognosis. We have precisely mapped regions of recurrent losses at 3p and gains at 3q25-qter in a series of lung SCC (GSE14859) amd moreover uncover 3q26.3-q27 high level amplifications in 20% of tumours. These amplicons were precisely mapped in these tumors using arraCGH with a 3q26.3 dedicated tiling array. Keywords : ArrayCGH, lung Squamous Cell Carcinoma, 3q26.3, SOX2 Keywords: ArrayCGH Profiling of 5 advanced (stage III) lung SCC using a chromosome 3 array providing 3q26.3-q27 tiling coverage. Replicates : each array contains three replicates per clone and each sample is hybridized to two arrays, results are subsequently averaged.

2010-02-09 | E-GEOD-15079 | biostudies-arrayexpress

ArrayCGH mapping of chromosome 3 aberrations in lung Squamous Cell Carcinoma (SCC)

2010-02-10 | GSE14859 | GEO

ArrayCGH mapping of the recurrent 3q26.3-q27 amplifications in lung Squamous Cell Carcinoma (SCC)

2010-02-10 | GSE15079 | GEO

Detection of Cancer with Serum miRNAs on an Oligonucleotide Microarray

Project description:Micro RNAs (miRNAs) are a class of small, non-coding RNA species that play critical roles throughout cellular development and regulation. miRNA expression patterns taken from various tissue types often point to the cellular lineage of an individual tissue Arrays for serum miRNA analysis were constructed with 547 human miRNA sequences obtained from the Sanger Database version 10.0 which appeared on 8/2/07. Because of limited space on the array, the probe list was modified to exclude a few newer miRNAs that had recently been added. The array includes miRNA probes for all studies referenced by this paper. Three probes were written for each miRNA: an anti-sensed wild-type version, a double-mutant control probe, and a sense control version. Antisense controls were not included if the corresponding antisense miRNA existed in the databases. The double mutant control mutations were screened in order to maintain the same notional melting temperature (Tm) as the wild-type Tm. They were also designed to avoid perturbing or creating any secondary structure that might appear in the wild-type probe. In addition to the 547 human miRNAs, we also included as controls, four sheep, three C. elegans, and two human sequences.

2010-06-24 | E-GEOD-16512 | biostudies-arrayexpress

Homo sapiens

Project description:ArrayCGH mapping of chromosome 3 aberrations in lung Squamous Cell Carcinoma (SCC)

| PRJNA123187 | ENA

Gene Expression Data of Hibernating and Summer Active Black Bears

Project description:We conducted a large-scale gene expression screen using the 3,200 cDNA probe microarray developed specifically for Ursus americanus to detect expression differences in liver and skeletal muscle that occur during winter hibernation in comparison to animals sampled during summer. The expression of 12 genes, including RNA binding protein motif 3 (Rbm3), that are mostly involved in protein biosynthesis, was induced during hibernation in both liver and muscle. The Gene Ontology and Gene Set Enrichment analysis consistently showed a highly significant enrichment of the protein biosynthesis category by over-expressed genes in both liver and skeletal muscle during hibernation. Coordinated induction in transcriptional level of genes involved in protein biosynthesis is a distinctive feature of the transcriptome in hibernating black bears. This finding implies induction of translation and suggests an adaptive mechanism that contributes to a unique ability to reduce muscle atrophy over prolonged periods of immobility during hibernation. Comparing expression profiles in bears to small mammalian hibernators shows a general trend during hibernation of transcriptional changes that include induction of genes involved in lipid metabolism and carbohydrate synthesis as well as depression of genes involved in the urea cycle and detoxification function in liver. Black bears sampled during winter hibernation were compared with the animals sampled during summer. Two tissue types, liver and muscle, were hybridized on a custom 3,200-gene nylon membrane microarray platform with three replicates for each gene (9.600 spots in total). Six hibernating and five summer active bears were studied in experiments with liver tissue, five hibernating and five summer active animals were tested with muscle tissue.

2009-03-09 | E-GEOD-15099 | biostudies-arrayexpress

MicroRNA Expression Profile Reveals Important Clinical Tools for the Pathology of Lung Cancer

Project description:We investigated whether the miRNA expression could distinguish lung cancers from normal tissues, examining 116 pairs of primary lung cancers with their corresponding adjacent normal lung tissues collected a minimum of 5 cm from the tumor. Our analysis identified a five microRNA classifier could distinguish malignant lung cancer lesions from adjacent normal tissues. SCLC could be distinguished from non small lung cancer by microRNAs profiling. Survival associations were examined with the SCC and adenocarcinoma subtypes. High hsa-miR-31 expression was associated with poor survival in SCC, and the association was confirmed in 20 independent SCC patients by qRT-PCR assays. Overall these findings may help advance the use of microRNA profiling in personalized diagnosis of lung cancers. Key Words: microRNA; lung cancer; microarray; diagnosis; prognosis cancer vs adjacent normal tissues

2010-02-10 | E-GEOD-15008 | biostudies-arrayexpress

Gene Expression Profiles of PBMC Subsets in Acute GVHD Following Cord Blood Transplantation (IMS v.1)

Project description:In comparison with allogeneic hematopoietic stem cell transplantation using other sources, umbilical cord blood transplantation (UCBT) offers substantial clinical advantages including a lower incidence and severity of acute graft-versus-host disease (GVHD) despite the use of allogeneic UCB stem cells with more disparate HLA. However, detailed pathophysiology of acute GVHD developed after UCBT has not yet been clarified. Here, we examined the roles of inflammatory cells in the pathogenesis of acute GVHD following UCBT, by expression profiling of a total of 595 genes in each of 4 subsets (CD4+, CD8+, CD14+, and CD56+) of peripheral blood mononuclear cells (PBMCs), which were taken from 3 patients with hematologic malignancy, in whom acute GVHD had developed after UCBT. We compared expression profiles measured during acute GVHD with those measured opon discharge (recovery phase), for each subset of PBMCs to identify immuno-regulatory genes which were assumed to be linked to the pathogenesis of acute GVHD. Keywords: disease state analysis Peripheral blood mononuclear cells (PBMCs) were taken from 3 patients with hematologic malignancy, in whom acute GVHD had developed after cord blood transplantation. CD4+, CD8+, CD14+, and CD56+ cell subsets were isolated from the PBMCs of 2 patients, while only CD8+ and CD56+ cell subsets were isolated from the PBMCs of a patient. PBMCs were taken twice - during acute GVHD phase and upon discharge (recovery phase), from each patient. By using a custom-made fibrous oligonucleotide DNA microarray Genopal (Mitsubishi Rayon), we compared expression profiles of 595 unique genes measured during acute GVHD with those measured upon discharge (recovery phase), for each subset of PBMCs.

2010-05-15 | E-GEOD-10512 | biostudies-arrayexpress

LSCC

Project description:The basaloid carcinoma (pure) and the (mixed) basalod variant of lung squamous cell carcinoma (SCC) have a dismal prognosis but their underlying specific molecular characteristics remain obscure and no therapy has proven to be efficient. In order to assess their molecular specificity among other lung squamous cell carcinomas we analysed DNA copy number aberrations and mRNA expression pangenomic profiles of 93 SCC, including 42 basaloid samples (24 pure, 18 mixed).

2014-11-17 | E-MTAB-2435 | biostudies-arrayexpress

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