Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Comparative genomic hybridization of frozen salivary or pulmonary adenoid cystic carcinoma samples and normal tissue to identify copy number alterations

ABSTRACT: Adenoid cystic carcinoma (AAC) is a rare but distinctive tumor. Array comparative genomic hybridization (CGH) has been applied for detecting chromosomal copy number alterations in seventeen frozen salivary or pulmonary ACCs samples. There were recurrent gains at 1p36, 6p21, 16q24, 17q21, and 22q11-13, and recurrent losses at 1p35, 6q22, 8q12-13, 9p21, 12q12-13, and 17p11-13. The minimal common regions (MCRs) of these alterations contained several well-known cancer genes, including TP53, CDKN2A/CDKN2B, SKI, CDK10, and VEGF. CDK10 was the only oncogene that localized to the MCR of gain at 16q24.1-24.3. In addition, we identified LIMA1 as the sole putative tumor suppressor gene residing in the MCR of deletion at 12q12q12-13.2. Among well defined and narrow, but unique alterations, there were gains harboring MDM2, cyclin D1, and KIT, as well as one loss involving the hsa-mir-124a-2 miRNA. Using immunohistochemistry, we found abnormal protein expression in the cases with gain of cyclin D1 or MDM2. In conclusion, the majority of previously reported chromosomal copy number alterations are found using array CGH in this small cohort. The suspicion that genes such as TP53, CDKN2A/CDKN2B, and VEGF might play a role in ACC, is strengthened by our results. CDK10 and LIMA1 emerge from our analysis as candidate cancer genes

ORGANISM(S): Homo sapiens

SUBMITTER: Philippe Dessen

PROVIDER: E-TABM-267 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

High-resolution array comparative genomic hybridization analysis of human bronchial and salivary adenoid cystic carcinoma.

Bernheim Alain A Toujani Saloua S Saulnier Patrick P Robert Thomas T Casiraghi Odile O Validire Pierre P Temam Stéphane S Menard Philippe P Dessen Philippe P Fouret Pierre P

Laboratory investigation; a journal of technical methods and pathology 20080310 5

Adenoid cystic carcinoma (ACC) is a rare but distinctive tumor. Oligonucleotide array comparative genomic hybridization has been applied for cataloging genomic copy number alterations (CNAs) in 17 frozen salivary or bronchial tumors. Only four whole chromosome CNAs were found, and most cases had 2-4 segmental CNAs. No high level amplification was observed. There were recurrent gains at 7p15.2, 17q21-25, and 22q11-13, and recurrent losses at 1p35, 6q22-25, 8q12-13, 9p21, 12q12-13, and 17p11-13. T ...[more]

PMID: 18332873

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Project description:Therapy-related acute myeloid leukemia (t-AML) is a severe complication of the cytotoxic therapy used for primary cancer treatment. The outcome of these patients is poor compared to people who develop de novo acute myeloid leukemia (p-AML). Chromosome abnormalities in t-AML are partly dependent on the induction agent. Partial or total losses of chromosome 5 and/or 7 are observed after therapy with alkylating agents. Balanced translocations, most of which involve 11q23 with MLL rearrangement, are found after treatment with the topoisomerase II inhibitor. Complex cases are also more frequent. The aim of this study was to compare t-AML to p-AML using high-resolution array CGH in order to identify gene-specific copy number abnormalities (CNA). Thirty t-AML versus thirty-six p-AML patient samples were studied. In t-AML, 99 CNAs were observed with 63 losses and 36 gains while the mean number was 3,3 per case. In p-AML, 64 CNAs were observed with 30 losses and 34 gains with a mean number of 1.78 per case. A few very complex cases (>8 chromosomal abnormalities) contributed considerably to the chromosomal burden in p-AML. Several minimal critical regions (MCR) that contain proteins and microRNA genes implicated in leukemogenesis were found in t-AML. On 7p15.2, a HOXA gene cluster involved in the processes of hematopoietic progenitor cell development and leukemogenesis was recurrently gained. Loss of a 5 Mb MCR located on 5q31.3q32 (142,91-148,19 Mb) was found distal to a previously described MCR; it harbored 29 genes. A 40kb deleted MCR pointed to RUNX1 on 21q22, a gene coding for a transcription factor implicated in frequent rearrangements in leukemia and in familial thrombocytopenia with susceptibility to AML. The sequence revealed no abnormality in 3 patients and a mutation in one patient, resulting in complete deficiency of RUNX1. In de novo AML a gain of 21q22<38,41-39,36> harboring ERG and ETS2 was observed in two patients with very complex rearrangements.

Dataset Information

Comparative genomic hybridization of frozen salivary or pulmonary adenoid cystic carcinoma samples and normal tissue to identify copy number alterations

Publications

High-resolution array comparative genomic hybridization analysis of human bronchial and salivary adenoid cystic carcinoma.

Similar Datasets

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