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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression signature associated with BRAFV600E mutation in human papillary thyroid carcinoma based on transgenic mouse model (human)

ABSTRACT: BRAFV600E mutation is the most frequent molecular event in papillary thyroid carcinoma. The relation of this genetic alteration with the factors od poor prognosis has been reported as well as its influence on PTC gene signature. However human material disables distinction of cancer causes from its effect. We used our transgenic mouse model of papillary thyroid carcinoma induced by the BRAFV600E mutation to select BRAFV600E-specifi gene signature which was than compared to human material The human microarray data were obtained for: 27 papillary thyroid carcinomas including 18 BRAF(+), 8 RET(+), 1 RAS(+); 18 apparently healthy thyroids. In order to find BRAFV600E-specific gene signature data obtained from our transgenic mouse model of PTC were compared to human material. The analyses were performed taking into account not only the BRAF mutation but also other PTC initiating events including RET rearrangements and RAS poin mutations. Morover the microarray data were validated with the QPCR reaction.

ORGANISM(S): Homo sapiens

SUBMITTER: Michal Swierniak

PROVIDER: E-GEOD-58545 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression signature associated with BRAFV600E mutation based on transgenic mouse model (mouse)

Project description:BRAFV600E mutation is the most frequent molecular event in papillary thyroid carcinoma. The relation of this genetic alteration with the factors od poor prognosis has been reported as well as its influence on PTC gene signature. However human material disables distinction of cancer causes from its effect. We used our transgenic mouse model of papillary thyroid carcinoma induced by the BRAFV600E mutation to select BRAFV600E-specific gene signature The transgenic mouse model was obtained by the microinjection of the transgene, composed of the human BRAF cDNA with V600E mutation under the control of bovine thyroglobulin, into the ferilized mice egg cells. Three lines were derived and mice after 4-24 months were sacrificed and histopathological evaluation of thyroids was carried out. In order to find BRAFV600E-specific gene signature microarray analysis was performed. The analysis invloved 38 mice thyroid samples: 10 mice papillary thyroid carcinomas, 10 borderline lesions (all being BRAF-positive), 10 apparently asymptomatic thyroids (5 BRAF-positive and 5 BRAF-negative) and 8 benign hyperplastic lesions (4 BRAF-positive and 4 BRAF-negative). Multofactoral analyses were performed in order to define some additional factors that could have impact on the gene expression profile.

2015-12-31 | E-GEOD-58546 | biostudies-arrayexpress

Gene expression signature associated with BRAFV600E mutation in human papillary thyroid carcinoma based on transgenic mouse model (human)

2015-12-31 | GSE58545 | GEO

Gene expression signature associated with BRAFV600E mutation based on transgenic mouse model (mouse)

2015-12-31 | GSE58546 | GEO

Gene expression profiles in BCPAP cells treated with BRAF inhibitors

Project description:We performed gene expression profiling in the human papillary thyroid carcinoma (PTC) derived cell line BCPAP harboring BRAFV600E mutation following the treatment with BRAF selective inhibitors.

2021-07-13 | GSE171483 | GEO

Gene expression profiling associated with the progression to poorly differentiated thyroid carcinomas

Project description:Poorly differentiated thyroid carcinomas (PDTC) represent a heterogeneous, aggressive entity, presenting features that suggest a progression from well-differentiated carcinomas. To elucidate the mechanisms underlying such progression and identify novel therapeutical targets, we assessed the genome-wide expression in normal thyroid tissues, well-differentiated thyroid carcinomas and PDTC. RNA were extracted from 2 normal thyroid tissues taken from the opposite lobe of thyroid tumors, and 24 thyroid carcinomas: 5 PDTC, 7 classic papillary thyroid carcinomas (cPTC), 8 follicular variants of PTC (fvPTC) and 4 follicular thyroid carcinomas (FTC). All samples were obtained at time of surgery and immediately frozen in liquid nitrogen. We also hybridized a commercial pool of human thyroid total RNA (BD Bioscience). PTC were screened for BRAF mutations and rearrangements of RET/PTC and, in addition, follicular variants were also analyzed for RAS mutations and PAX8-PPARG rearrangements. FTC were screened for RAS and PAX8-PPARG rearrangements. PDTC were analyzed for BRAF, RAS and PAX8-PPARG genes.

2013-12-10 | E-GEOD-53157 | biostudies-arrayexpress

Human thyroid adenomas, carcinomas, and normals

Project description:Human samples of various thyroid carcinomas, adenomas, and normals, each from a different patient, had mRNA assays performed using Affymetrix HG_U133A arrays, with 22283 probe-sets. The 99 samples consisted of 4 normals, 10 follicular adenomas, 13 follicular carcinomas, 7 oncocytic adenomas, 8 oncocytic carcinomas, 51 papillary carcinomas (each typed as having classical, follicular or tall cell morphology), 4 anaplastic carcinomas, and 2 medullary carcinomas. Interesting additional information on common mutations are provided including RAS mutation, BRAF mutation, RET/PTC rearrangements, and PAX8/PPARG translocations. Details of those assays are provided in our linked publications, as well as additional details on the specific mutations in a few special cases. No survival data is provided. Information for 93 of the 99 samples was previously made available on the web. The anaplastic and medullary carcinoma data were not previously shared. A supplementary Excel spreadsheet holding the same processed data as the series matrix file is provided and is more compact. The raw (.CEL) files are also provided. Human samples of various thyroid carcinomas, adenomas, and normals. The 99 samples consisted of 4 normals, 10 follicular adenomas, 13 follicular carcinomas, 7 oncocytic adenomas, 8 oncocytic carcinomas, 51 papillary carcinomas (each typed as having classical, follicular or tall cell morphology), 4 anaplastic carcinomas, and 2 medullary carcinomas. Additional information on common mutations are provided including RAS mutation, BRAF mutation, RET/PTC rearrangements, and PAX8/PPARG translocations.

2011-02-09 | E-GEOD-27155 | biostudies-arrayexpress

Proteogenomics analysis unveils a novel TFG-RET gene fusion and druggable targets in papillary thyroid carcinomas

Project description:Papillary thyroid cancer (PTC) is the most common type of endocrine malignancy. From a set of PTC patients whose tumor did not harbour any BRAF or RAS mutations, a 35 years old male patient’s normal, primary tumor and lymph node (LN) metastatic tissues were subjected to genomics and proteomics analysis. By RNA-seq analysis, we identified a novel RET rearrangement involving exons 1-4 from the 5’ end of the Trk fused Gene (TFG) fused to the 3’ end of RET tyrosine kinase leading to a TFG-RET fusion which transforms immortalized human thyroid cells in a kinase-dependent manner. Further, TFG-RET oncogene oligomerises in a PB1 domain-dependent manner and consistently, mutation of the oligomerisation interface led to the inhibition of RET-mediated oncogenic transformation. Quantitative proteomic analysis of the same samples revealed the upregulation of proteins involved in the ubiquitination machinery including E3 Ubiquitin ligase HUWE1 and DUBs like USP9X and UBP7 in both tumor and LN metastatic lesions. We further identified that expression of TFG-RET led to the upregulation of HUWE1. Further, in a cohort of PTC patients, we observed higher expression of HUWE1, USP9X and USP7 in the tumor and metastatic lesions, when compared to the matched normal tissue. Transient knockdown of HUWE1, USP9X and USP7 affected viability and proliferation of TFG-RET transformed cells. Consistently, inhibition of RET, HUWE1 and DUBs by small molecule inhibitors significantly reduced RET-mediated oncogenesis. Apart from unveiling a novel oncogenic RET fusion in PTCs, our data may open a novel avenue of targeting ubiquitin signaling machinery in human PTCs.

2020-04-02 | PXD016828 | Pride

MicroRNA profiling of human papillary thyroid carcinoma and normal thyroid to assess the role of miRNA genes in papillary thyroid carcinoma

Project description:Apart from alterations in the RET/PTC-RAS-BRAF pathway, comparatively little is known about the genetics of papillary thyroid carcinoma (PTC). We show that numerous miRNAs are transcriptionally up-regulated in PTC tumors compared with unaffected thyroid tissue. A set of 5 miRNAs including the 3 most upregulated ones (miRs 221, 222, 146) distinguished unequivocally between PTC and normal thyroid. Additionally, miR-221 was upregulated in unaffected thyroid tissue in several PTC patients, presumably an early event in carcinogenesis. Tumors in which the upregulation (11-19 fold) of miRs 221, 222 and 146 was strongest showed dramatic loss of KIT transcript and Kit protein. In five of 10 such cases this was associated with germline single nucleotide changes in the two recognition sequences in KIT for these miRNAs. We conclude that upregulation of several miRs and down regulation of KIT are involved in PTC pathogenesis, and that sequence changes in genes targeted by miRNAs can contribute to their downregulation.

2005-02-28 | E-TABM-68 | biostudies-arrayexpress

Proteogenomics analysis unveils a novel TFG-RET gene fusion and druggable targets in papillary thyroid carcinomas

Project description:Papillary thyroid cancer (PTC) is the most common type of endocrine malignancy. From a set of PTC patients whose tumor did not harbour any BRAF or RAS mutations, a 35 years old male patient’s normal, primary tumor and lymph node (LN) metastatic tissues was subjected to genomics and proteomics analysis. By RNA-seq analysis, we identified a novel RET rearrangement involving exons 1-4 from the 5’ end of the Trk fused Gene (TFG) fused to the 3’ end of RET tyrosine kinase leading to a TFG-RET fusion which transforms immortalized human thyroid cells in a kinase dependent manner. Further, TFG-RET oncogene oligomerises in a PB1 domain dependent manner and consistently, mutation of the oligomerisation interface led to the inhibition of RET-mediated oncogenic transformation. Quantitative proteomic analysis of the same samples revealed the upregulation of proteins involved in the ubiquitination machinery including HECT carrying E3 Ubiquitin ligase HUWE1 and DUBs like USP9X and UBP7 in the tumor and LN metastatic lesions. We further identify that expression of TFG-RET led to the upregulation of HUWE1. Further, in a cohort of PTC patients, we observed higher expression of HUWE1, USP9X and USP7 in the tumor and metastatic lesions, when compared to the matched normal tissue. Transient knockdown of HUWE1, USP9X and USP7 affected viability and proliferation of TFG-RET transformed cells. Consistently, inhibition of RET, HUWE1 and DUBs by small molecule inhibitors significantly reduced RET-mediated oncogenesis. Apart from unveiling a novel oncogenic RET fusion in PTCs, our data may open a novel avenue of targeting ubiquitin signaling machinery in human PTCs.

2020-04-02 | PXD016739 | Pride

miRNA profile induced by RET/PTC1 oncogene in human thyrocytes

Project description:To obtain a PTC cell model, primary human thyrocytes have been infected with a retrovirus expressing RET/PTC1 oncogene, using parental thyrocytes as control. The obtained RET/PTC-dependent differential miRNA expression profile, representing the effects of RET/PTC1 oncogene present in about one third of papillary thyroid carcinoma (PTC), models the early event of thyrocytes transformation ending to PTC.

2014-06-30 | GSE49400 | GEO

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