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ArrayCGH mapping of the recurrent 3q26.3-q27 amplifications 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. 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

ORGANISM(S): Homo sapiens

PROVIDER: GSE15079 | GEO | 2010/02/10

SECONDARY ACCESSION(S): PRJNA123213

REPOSITORIES: GEO

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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 chromosome 3 aberrations 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. 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.

2010-05-14 | E-GEOD-14859 | biostudies-arrayexpress

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

Homo sapiens

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

| PRJNA123187 | ENA

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

Diverse routes to oral cancer differing in genome instability and risk for cervical node metastasis

Project description:Clinically evident oral lesions, oral epithelial dysplasia, precede development of oral squamous cell carcinomas (SCC) and are considered to transform to cancer by acquisition of genetic or epigenetic alterations. Here, we show that, +3q24-qter, -8pter-p23.1, +8q12-q24.2 and +20 are early events identifying two pathways to oral cancers that differ in clinical behavior. One or more of these copy number aberrations is present in the major subgroup (3q8pq20 subtype, 75-80% of lesions) that develops with chromosomal instability and risk for metastasis, while they are absent from the smaller and chromosomally stable non-3q8pq20 subgroup (20-25% of lesions) associated with low risk for metastasis. Thus, +3q, -8p, +8q and +20 is a biomarker for oral SCC metastasis. On the other hand, while increased numbers of genomic alterations can be harbingers of progression to cancer, dysplastic lesions lacking copy number changes cannot be considered benign as they are potential precursors to non-3q8pq20 oral SCC. 63 oral SCCs and adjacent regions of normal tissue, 44 oral dysplasias

2011-11-18 | E-GEOD-28407 | biostudies-arrayexpress

Diverse routes to oral cancer differing in genome instability and risk for cervical node metastasis

2011-11-18 | GSE28407 | GEO

DNA copy number variation profiling and transcription profiling by array of 93 human lung squamous cell carcinoma samples

Project description:The basaloïd carcinoma (pure) and the basaloïd variant of lung squamous cell carcinoma (SCC) have a dismal prognosis but their underlying specific molecular characteristics remain obscure. This experiment uses DNA copy number aberrations and mRNA expression pangenomic profiles of 93 SCC, including 42 basaloïd samples (24 pure, 18 mixed) to reveal that pure basaloid tumors display a specific mRNA expression profile, encoding factors controlling the cell cycle, transcription, chromatin and splicing, with prevalent expression in germline and stem cells, while genes related to squamous differentiation are underexpressed. The related study demonstrates, for the first time, that basaloïd SCC constitute a distinct histo-molecular entity, which justifies its histologic recognition and distinction from SCC NOS. Additionally, their characteristic molecular profile highlights their intrinsic resistance to cytotoxic chemotherapy and could serve as a guide for targeted therapies.

2014-10-03 | E-MTAB-1727 | biostudies-arrayexpress

Gene expression profiling of asbestos-related lung squamous cell carcinoma

Project description:To identify gene expression biomarkers associate with asbestos-related lung squamous cell carcinoma, we analyzed gene expression profiles for a total of 56 lung squamous cell carcinomas using 44K Illumina Gene Expression microarrays. Twenty-six cases had lung asbestos body counts above levels associated with urban dwelling (ARLC-SCC: asbestos-related lung cancer-squamous cell carcinoma) and 30 cases had no lung asbestos bodies (NARLC-SCC: non-asbestos related lung cancer- squamous cell carcinoma). Genes differentially expressed between ARLC-SCC and NARLC-SCC were identified on fold change and P-value, and then prioritised using gene ontology.

2012-01-30 | GSE23822 | GEO

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