Expression data from primary and hereditary pheochromocytomas (PHEOs) and paragangliomas (PGLs)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE50442 | GEO | 2013/12/31
SECONDARY ACCESSION(S): PRJNA217505
REPOSITORIES: GEO
Similar Datasets
Project description:Genotype specific differences in expression profiles have been evaluated using human HuGene1.0-ST Gene Chips. In this dataset we include expression data for 7 PHEOs/PGLs patient samples with HIF2A or PHD2 mutation. Viable appearing tissue from the center of the lesions was collected and snap frozen for RNA extraction. Each of the 7 PHEO/PGL samples was examined by pathologist upon resection. Microarray analysis was performed on normal and tumor samples.
2013-12-31 | E-GEOD-50442 | biostudies-arrayexpress
Project description:Genotype specific differences in expression profiles have been evaluated using human HuGene1.0-ST Gene Chips. In this dataset we include expression data obtained from 8 normal adrenal medulla and 45 PHEOs/PGLs patient samples. Viable appearing tissue from the center of the lesions was collected and snap frozen for RNA extraction. Each of the 45 PHEO/PGL samples was examined by pathologist upon resection. Patients PKh_27 and PKh_28 with SDHB mutation were from the same patient with samples taken from two different locations at different times. Diagnosis of PHEO/PGL has been confired in all cases histopathologically. The tissues were grouped according to genetic/syndromic background and tumor location into SDHB (n = 18), SDHD-A/T (n = 6), SDHD-HN (n= 8), and VHL (n = 13).
2013-11-12 | GSE39716 | GEO
Project description:Genome-scale DNA methylation was analyzed in a large cohort of pheochromocytomas and paragangliomas (PCC/PGL). Consensus clustering identified 3 stable clusters significantly associated with expression subgroups, gene mutations, and clinical parameters. Bisulfite-converted DNA from 145 fresh frozen PCC/PGL and 3 normal adrenal medulla samples were hybridized to Illumina Infinium 27k Human Methylation BeadChips.
2013-05-06 | E-GEOD-39198 | biostudies-arrayexpress
Project description:Genome-scale DNA methylation was analyzed in a large cohort of pheochromocytomas and paragangliomas (PCC/PGL). Consensus clustering identified 3 stable clusters significantly associated with expression subgroups, gene mutations, and clinical parameters.
2013-05-06 | GSE39198 | GEO
Project description:Genotype specific differences in expression profiles have been evaluated using human HuGene1.0-ST Gene Chips. In this dataset we include expression data obtained from 8 normal adrenal medulla and 45 PHEOs/PGLs patient samples. Viable appearing tissue from the center of the lesions was collected and snap frozen for RNA extraction. Each of the 45 PHEO/PGL samples was examined by pathologist upon resection. Patients PKh_27 and PKh_28 with SDHB mutation were from the same patient with samples taken from two different locations at different times. Diagnosis of PHEO/PGL has been confired in all cases histopathologically. The tissues were grouped according to genetic/syndromic background and tumor location into SDHB (n = 18), SDHD-A/T (n = 6), SDHD-HN (n= 8), and VHL (n = 13). Microarray analysis was performed on normal and tumor samples. We used PAM model to identify minimum subset of genes selective for each mutation class. Heirarchical cluster analysis was used to identify samples with similar expression patterns. Data was validated using qRT-PCR analysis.
2013-11-12 | E-GEOD-39716 | biostudies-arrayexpress
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.
2012-03-23 | GSE32204 | GEO
Project description:8658860258318000Recently, genetic alterations in the genes encoding succinate dehydrogenase subunit B and D (SDHB and SDHD) were identified in pet dogs that presented with spontaneously arising pheochromocytomas (PCC) and paragangliomas (PGL; together PPGL), suggesting dogs might be an interesting comparative model for the study of human PPGL. To study whether canine PPGL resembled human PPGL, we investigated a series of 50 canine PPGLs by immunohistochemistry to determine the expression of synaptophysin (SYP), tyrosine hydroxylase (TH) and succinate dehydrogenase subunit A (SDHA) and B (SDHB). In parallel, 25 canine PPGLs were screened for mutations in SDHB and SDHD by Sanger sequencing. To detect large chromosomal alterations, single nucleotide polymorphism (SNP) arrays were performed for 11 PPGLs, including cases for which fresh frozen tissue was available. The immunohistochemical markers stained positive in the majority of canine PPGLs. Genetic screening of the canine tumors revealed the previously described variants in four cases; SDHB p.Arg38Gln (n = 1) and SDHD p.Lys122Arg (n = 3). Furthermore, the SNP arrays revealed large chromosomal alterations of which the loss of chromosome 5, partly homologous to human chromosome 1p and chromosome 11, was the most frequent finding (100% of the six cases with chromosomal alterations). In conclusion, canine and human PPGLs show similar genomic alterations, suggestive of common interspecies PPGL-related pathways.
| S-EPMC6563419 | biostudies-literature
Project description:Paragangliomas (PGL) and pheochromocytomas (PCC) are rare, usually benign tumors that originate from the neuroendocrine tissue along the paravertebral axis. Up to 35% of these tumors may be hereditary; they are associated with germline mutations in genes encoding subunits of the succinate dehydrogenase (SDH) enzyme complex in the context of the familial PGL syndromes, PGL1, 3 and 4 caused by mutations in the SDHD,SDHC and SDHB genes, respectively. Another familial PGL syndrome, PGL2, is caused by mutations in SDHAF2/SDH5, which encodes for a molecule that is an accessory to the function of the SDH enzyme and its SDHA subunit. Less frequently, mutations in the genes responsible for Von Hippel Lindau disease (VHL), multiple endocrine neoplasia type 2 (MEN2), and neurofibromatosis type 1 (NF1) are also found in patients with hereditary PGL and PCC. Recently mutations were found in the SDHA subunit in a limited number of patients with PGL and/or PCC. The SDHB, SDHC and SDHD gene mutations (but not SDHA) can also be found in patients with PGL and/or PCC and gastrointestinal stromal tumors (GISTs), also known as the Carney-Stratakis syndrome; SDHB mutations, in particular, may also predispose to thyroid and renal cancer, and possibly other tumors. A new gene was recently found to predispose to PGL and/or PCC when mutated is TMEM127. In this text, we provide an overview of the genetics of PGLs and related conditions with an emphasis on genetic risk assessment, prevention, and prognosis.
| S-EPMC4221053 | biostudies-literature
Project description:A Cartes d'Identité des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net): Pheochromocytomas (PCC) and paragangliomas (PGL) are neural crest-derived tumors. We performed the integrated genomic analysis of a collection of PCC/PGL from the French COMETE network using SNP arrays, whole-exome sequencing, DNA methylation arrays, mRNA expression arrays and miRNA sequencing. We found that PCC/PGL are characterized by a low mutation rate, with few recurrent somatic mutations and focal copy number alterations (CNAs). In contrast, we detected recurrent broad CNAs strongly associated with known molecular groups, often leading to the biallelic inactivation of the known susceptibility genes of PCC/PGL. We also identified DNA methylation changes and miRNA expression clusters strongly associated with molecular groups. Of note, overexpression of the miRNA cluster 182/96/183 is specific of SDHB-mutated tumors and induces invasive traits, whereas silencing of the imprinted DLK1-MEG3 miRNA cluster due to a loss of heterozygosity of the 14q32.2 locus is a potential driver in a subset of sporadic tumors. This comprehensive analysis illustrates the functional interdependence between genomic and epigenomic dysregulations underlying PCC/PGL.
2015-02-02 | E-MTAB-2817 | biostudies-arrayexpress
Project description:A Carte d'Identitite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net): Pheochromocytomas (PCC) and paragangliomas (PGL) are neural crest-derived tumors. We performed the integrated genomic analysis of a collection of PCC/PGL from the French COMETE network using SNP arrays, whole-exome sequencing, DNA methylation arrays, mRNA expression arrays and miRNA sequencing. We found that PCC/PGL are characterized by a low mutation rate, with few recurrent somatic mutations and focal copy number alterations (CNAs). In contrast, we detected recurrent broad CNAs strongly associated with known molecular groups, often leading to the biallelic inactivation of the known susceptibility genes of PCC/PGL. We also identified DNA methylation changes and miRNA expression clusters strongly associated with molecular groups. Of note, overexpression of the miRNA cluster 182/96/183 is specific of SDHB-mutated tumors and induces invasive traits, whereas silencing of the imprinted DLK1-MEG3 miRNA cluster due to a loss of heterozygosity of the 14q32.2 locus is a potential driver in a subset of sporadic tumors. This comprehensive analysis illustrates the functional interdependence between genomic and epigenomic dysregulations underlying PCC/PGL.
2015-02-02 | E-MTAB-2833 | biostudies-arrayexpress