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DNA methylation profiling in pheochromocytoma and paraganglioma reveals diagnostic and prognostic markers

ABSTRACT: A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net):we explored DNA methylation patterns associated with PPGL malignancy using two large and well characterized cohorts of PPGL collected through a multi-institutional collaboration through the European Network for the Study of Adrenal Tumors (ENS@T). Bisulfite converted DNA from fresh frozen paragangliomas and adrenal medulla samples were hybridized to Illumina Infinium 27k Human Methylation

ORGANISM(S): Homo sapiens

SUBMITTER: Nabila Elarouci

PROVIDER: E-GEOD-62082 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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DNA methylation profiling in pheochromocytoma and paraganglioma reveals diagnostic and prognostic markers

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net):we explored DNA methylation patterns associated with PPGL malignancy using two large and well characterized cohorts of PPGL collected through a multi-institutional collaboration through the European Network for the Study of Adrenal Tumors (ENS@T).

2015-05-11 | GSE62082 | GEO

Genome-scale methylome profiling of pheochromocytomas and paragangliomas with Illumina HumanMethylation450 arrays

Project description:Genome-scale DNA methylation was analyzed in a cohort of paragangliomas to identify DNA methylation changes. Bisulfite converted DNA from 22 fresh frozen paragangliomas and 2 normal adrenal medulla samples were hybridized to Illumina HumanMethylation450 BeadChips.

2013-05-06 | E-GEOD-43293 | biostudies-arrayexpress

Epigenome analysis of pheochromocytoma/paraganglioma samples (II)

Project description:Genome wide DNA methylation profiling of pheochromocytoma/paraganglioma samples carrying different mutations. The Illumina Infinium EPIC Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 850,000 CpGs. The main goal of this project was to find specific methylation profiles associated to the presence of mutations in the different genetic sub-classes of pheochromocytomas/paragangliomas.

2020-06-15 | GSE123185 | GEO

Whole transcriptome analysis of canine pheochromocytoma and paraganglioma

Project description:Pheochromocytomas and paragangliomas (PPGLs) are neuroendocrine tumors arising from the chromaffin cells in the adrenal medulla and extra-adrenal paraganglia, respectively. Local invasion, concurrent disorders, and in rare occasions metastases prevent surgical removal, which is the most effective treatment to date. Given the current lack of effective medical treatment, there is a need for novel therapeutic strategies. To identify druggable pathways driving PPGL development, we performed RNA sequencing on PPGLs (n=19) and normal adrenal medullas (NAMs; n=10) of dogs. Principal component analysis (PCA) revealed that PPGLs clearly clustered apart from NAMs. In total, 4,218 genes were differentially expressed between PPGLs and NAMs with a false discovery rate (FDR)-adjusted P value <0.05. Of these, 232 had a log2 fold change of >3 or <-3, of which 149 were upregulated in PPGLs, and 83 were downregulated. Compared with NAMs, PPGLs had increased expression of genes related to the cell cycle, tumor development, progression and metastasis, hypoxia and angiogenesis, and the Wnt signaling pathway, and decreased expression of genes related to adrenal steroidogenesis. Our data revealed several overexpressed genes that could provide targets for novel therapeutics, such as Ret Proto-Oncogene (RET), Dopamine Receptor D2 (DRD2), and Secreted Frizzled Related Protein 2 (SFRP2). Based on the PCA, PPGLs were classified into 2 groups, of which group 1 had significantly higher Ki67 scores (P=0.035) and worse survival times (P=0.04) than group 2. One of the differentially expressed genes (FDR-adjusted P value <0.1) between PPGL group 1 and 2, pleiotrophin (PTN), was significantly associated with survival (P=0.025).

2023-08-14 | GSE223526 | GEO

Genome-scale methylome profiling of pheochromocytomas and paragangliomas with Illumina Infinium 27k Human Methylation arrays

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

Expression profiles of pheochromocytoma and paraganglioma

Project description:Until now, it is nearly impossible to diagnose malignancy of peochormocytoma/paraganglioma with pathological examinations. The aim of the study is to find the genes which can be applied as a biomarker in the clinic to distinguish benign and malignant forms of pheochromocytoma/paraganglioma. We generated exprssion profiles of 9 samples of benign tumors, 3 samples of malignant tumors and 3 samples of normal adrenal medulla.

2014-08-17 | E-GEOD-60458 | biostudies-arrayexpress

Epigenome analysis of pheochromocytoma/paraganglioma samples

2018-12-11 | GSE111336 | GEO

AQP2 as a diagnostic immunohistochemical marker for pheochromocytoma and/or paraganglioma.

Project description:Background:Aquaporin2 (AQP2) is water channel protein that is widely distributed among mammalian tissues and plays a major role in water homeostasis. However, little is known about the expression and significance of AQP2 in human adrenal tumors. Thus, we performed an immunohistochemical investigation of AQP2 in normal and neoplastic adrenal tissues. Methods:AQP2 protein expression was investigated in 190 adrenal tumor patients using immunohistochemistry. Correlation between protein expression and clinicopathological features was statistically analyzed. Results:We demonstrated immunopositivity for AQP2 in all adrenal medulla-originating tumors, including 96 pheochromocytomas (PCC), 7 metastatic pheochromocytomas (MPCC), and 10 neuroblastic tumors (NT) and 13 extra-adrenal paragangliomas (EAPGL). Whereas, APQ2 was absent from the 52 adrenal cortical adenomas and 2 adrenal cortical carcinomas examined. The 10 metastatic carcinomas examined in adrenal tissue were also negative for AQP2. In 82 (85%) of the 96 samples from patients with PCC, we studied the relationship between clinicopathologic factors and AQP2 expression and our findings suggested that the tumors that exhibited diffuse expression pattern of AQP2 were larger in diameter than those exhibiting focal (P=0.007) or mediate expression pattern (P=0.001). Conclusions:AQP2 protein is significantly expressed in normal adrenal medullary tissues and medullary tumors (including PCC, MPCC and NT) as well as EAPGL. AQP2 expression may indicate the origin of normal adrenal tissues, and its expression in cancer tissue may reflect the maintenance of water metabolism via AQP2 during tumorigenesis. AQP2 may serve as a valuable marker for the differential diagnosis of adrenal tumors.

| S-EPMC7225480 | biostudies-literature

Expression data from pheochromocytoma (PHEO) and paraganglioma (PGL) tumor samples

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

Epigenome analysis of a paraganglioma sample carrying the DLST-p.Y422C mutation [methylation array]

Project description:Genome wide DNA methylation profiling of a paraganglioma sample carrying the DLST-p.Y422C mutation. The Illumina Infinium EPIC Human DNA methylation Beadchip v1.2 was used to obtain a DNA methylation profile across approximately 850,000 CpGs. The main goal of this project was to find specific methylation profiles associated to the presence of mutations in the DLST gene of pheochromocytomas/paragangliomas.

2023-05-05 | GSE210809 | GEO

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