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High-density genome-wide copy number variation (CNV) in human head and neck paragangliomas.

ABSTRACT: Gene-centric CNV analysis of 24 individual paraganglioma cases identified a list of 104 genes most significantly targeted by tumor-associated alterations. The NOTCH signaling pathway was the most significantly enriched term in the list. Overexpression of the relevant NOTCH pathway proteins in sustentacular (glial), chief (neuroendocrine) and endothelial cells was confirmed by immunomorphological studies in 47 paragangliomas, including CNV-tested cases. NOTCH upregulation was observed also in cases with no evidence of CNVs at NOTCH signaling genes, suggesting altered epigenetic modulation of the pathway. Notably, this was confirmed by microRNA expression analysis, that showed tumor-associated downregulation of the miR-200s and miR-34s families, correlated to NOTCH signaling and directly targeting NOTCH1.

ORGANISM(S): Homo sapiens

PROVIDER: GSE49614 | GEO | 2013/08/21

SECONDARY ACCESSION(S): PRJNA214468

REPOSITORIES: GEO

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High-density genome-wide copy number variation (CNV) in human head and neck paragangliomas.

Project description:Gene-centric CNV analysis of 24 individual paraganglioma cases identified a list of 104 genes most significantly targeted by tumor-associated alterations. The NOTCH signaling pathway was the most significantly enriched term in the list. Overexpression of the relevant NOTCH pathway proteins in sustentacular (glial), chief (neuroendocrine) and endothelial cells was confirmed by immunomorphological studies in 47 paragangliomas, including CNV-tested cases. NOTCH upregulation was observed also in cases with no evidence of CNVs at NOTCH signaling genes, suggesting altered epigenetic modulation of the pathway. Notably, this was confirmed by microRNA expression analysis, that showed tumor-associated downregulation of the miR-200s and miR-34s families, correlated to NOTCH signaling and directly targeting NOTCH1. Total DNA from paraganglioma sample compared to total DNA from paired blood sample.

2013-08-21 | E-GEOD-49614 | biostudies-arrayexpress

Genome-wide analysis of the miR profile in human head and neck paraganglioma vs. Jacobson's (tympanic) nerve and SH-SY5Y neuroblastoma cells

Project description:The aim of the study was to assess whether changes in the expression of miRs could be implicated in the modulation of the NOTCH pathway in head and neck paragangliomas. Several miRs, notably including families (miR-34s, miR-200s) that target the NOTCH signaling pathway, resulted differentially expressed in paragangliomas compared to the reference normal tissue, i.e., Jacobson's nerve. Total RNA from paraganglioma samples compared to total RNA from Jacobson's nerves (normal controls, chosen because Jacobson's nerve is a frequent site of origin of tympanic paraganglioma) and from SH-SY5Y cells (chosen based on their sympathoadrenal origin).

2013-08-21 | E-GEOD-49190 | biostudies-arrayexpress

Genome-wide analysis of the miR profile in human head and neck paraganglioma vs. Jacobson's (tympanic) nerve and SH-SY5Y neuroblastoma cells

2013-08-21 | GSE49190 | GEO

Project description:The similarity in gene-expression profiles suggest that PGL2, like SDHD, is involved in the functionality of the SDH complex, and that tumor formation in these three subgroups involves the same pathways as in SDH linked paragangliomas. We were not able to clarify the identity of PGL2 on 11q13. The lack of differential gene-expression of chromosome 11 genes might indicate that chromosome 11 loss, as demonstrated in SDHD-linked paragangliomas, is an important feature in the formation of a paraganglioma regardless of the genetic background. Keywords: disease state analysis We compared the gene expression profiles of sporadic (n=7), SDHD- (n=6) and PGL2-linked (n=4) head and neck paraganglioma.

2008-12-10 | E-GEOD-12921 | biostudies-arrayexpress

EPAS1-mutated paragangliomas are associated with hemoglobin disorders

Project description:This study reports a large series patients presenting EPAS1-mutated paraganglioma in whom we investigated a cause underlying chronic hypoxia. Four patients (10%) suffered from hypoxemic heart disease. In patients with available hemoglobin electrophoresis results, 59% presented a hemoglobin disorder. Histological and transcriptomic characterization of EPAS1-tumors revealed increased angiogenesis and high similarities with pseudohypoxic paragangliomas caused by VHL gene mutations.

2023-12-11 | GSE249273 | GEO

2008-12-10 | GSE12921 | GEO

Transcription profiling of pheochromocytomas and paragangliomas (188 tumor samples)

Project description:A Cartes d'Identité des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | Affymetrix HG-U133 Plus 2.0 : 188 tumor samples |Pheochromocytomas and paragangliomas are neuroendocrine tumors occuring in the context of inherited cancer syndromes in approximately 30% of cases, linked to germline mutations in VHL, RET, NF1, SDHA, SDHB, SDHC, SDHD, SDHAF2 or TMEM127 genes. Although progress has been made with regard to tumorigenesis mechanisms in pheochromocytoma/paraganglioma thanks to genome-wide expression studies, the question of a putative molecular distinction between VHL- and SDHx- on one hand, and RET- and NF1-related tumors on the other hand, remained to be addressed as well as the characterization of genetic events in sporadic tumors. With this purpose, 202 pheochromocytomas/paragangliomas, including 75 hereditary tumors, were investigated by expression profiling, array CGH and somatic mutation screening. The systematic characterization of somatic genetic events associated with tumor suppressor gene germline mutations in tumor tissues reveals a majority of loss of heterozygosity (LOH) but also point mutations and copy neutral LOH. Gene-expression signature defined the hereditary tumors according to their genotype. Especially, a complete sub-separation between SDHx- and VHL-related tumors was observed. Moreover, guided by the transcriptome classification and the LOH profile, somatic mutations in VHL or RET genes were identified in 14% of sporadic pheochromocytomas/paragangliomas. A genetic cause was found in 45.5% (92/202) of the large series of pheochromocytomas/paragangliomas analyzed. Regarding mutated genes, specific molecular pathways involved in tumorigenesis mechanisms are showed. Altogether, these new findings suggest that somatic mutation analysis would give important clues for personalized molecular target therapies.

2011-07-07 | E-MTAB-733 | biostudies-arrayexpress

SNP data from 78 pheochromocytomas and paragangliomas

Project description:SNP profiles from 78 pheochromocytomas and paragangliomas were analyzed to detect copy number changes and LOH.

2012-09-11 | GSE38525 | GEO

SNP data from 78 pheochromocytomas and paragangliomas

Project description:SNP profiles from 78 pheochromocytomas and paragangliomas were analyzed to detect copy number changes and LOH. 78 pheochromocytomas and paragangliomas were analyzed with Illumina Human610-Quad v1.0 BeadChips.

2012-09-11 | E-GEOD-38525 | biostudies-arrayexpress

SNP data from 30 pheochromocytomas and paragangliomas.

Project description:SNP profiles from 30 pheochromocytomas and paragangliomas were analyzed to detect identical-by-descent haplotypes, highlighting a founder mutation of SDHD in two samples. 30 pheochromocytomas and paragangliomas were analyzed with Illumina Human610-Quad v1.0 BeadChips.

2012-03-23 | E-GEOD-32204 | biostudies-arrayexpress

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