Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA339030 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4032860_1.fastq.gz | Fastqsanger.gz | |||
| SRR4032860_2.fastq.gz | Fastqsanger.gz | |||
| SRR4032870_1.fastq.gz | Fastqsanger.gz | |||
| SRR4032870_2.fastq.gz | Fastqsanger.gz | |||
| SRR4032861_1.fastq.gz | Fastqsanger.gz |
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Project description:Genomic binding of PAX8-PPARG fusion protein regulates cancer-related pathways and alters the immune landscape of thyroid cancer
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Project description:Genomic binding of PAX8-PPARG fusion protein regulates cancer-related pathways and alters the immune landscape of thyroid cancer [array]
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Project description:A chromosomal translocation results in production of an oncogenic PAX8-PPARG fusion protein (PPFP) in a subset of thyroid carcinomas. PAX8 is an important thyroid transcription factor, and PPARG is a transcription factor that plays important roles in the biology of adipocytes and macrophages, but has no known function in the thyroid. PPFP retains the DNA binding domains of both proteins. However, the genomic DNA binding sites of PPFP have not been identified, and only limited data exist to characterize gene expression in PPFP thyroid carcinomas. Therefore, we expressed PPFP in PCCL3 rat thyroid cells and used ChIP-seq to identify PPFP genomic binding sites (PPFP peaks) and RNA-seq to characterize PPFP-dependent gene expression. The genome contains ~20 000 PPFP peaks, including known PAX8 and PPARG binding sites, indicating that both DNA binding domains are functional. PPFP binds to and regulates many genes involved in cancer-related processes such as development and cell division. PPFP also binds to and regulates many genes related to mitochondria and lipid metabolism that are regulated by PPARG in adipocytes. Our data highlight the complexity of PPFP as a transcription factor and the numerous ways that it regulates thyroid oncogenesis.
2016-01-21 | GSE70354 | GEO
Project description:PAX8-PPARG fusion protein (PPFP) results from a t(2;3)(q13;p25) chromosomal translocation, is found in 30% of follicular thyroid carcinomas, and demonstrates oncogenic capacity in transgenic mice. A PPARG ligand, pioglitazone, is highly therapeutic in mice with PPFP thyroid carcinoma. We used our previously characterized transgenic mouse model of PPFP thyroid carcinoma to identify PPFP binding sites in vivo using ChIP-seq, and to identify genes and pathways regulated by PPFP with and without pioglitazone treatment via integration with RNA-seq and Affymetrix microarray data. This submission contains the Affymetrix microarray data. PPFP and pioglitazone regulated genes involved in lipid and fatty acid metabolism, ribosome function, immune processes, cell death and other cancer-related processes. The RNA-seq data yielded similar findings.
2016-12-21 | GSE85583 | GEO
Project description:PAX8-PPARG fusion protein (PPFP) results from a t(2;3)(q13;p25) chromosomal translocation, is found in 30% of follicular thyroid carcinomas, and demonstrates oncogenic capacity in transgenic mice. A PPARG ligand, pioglitazone, is highly therapeutic in mice with PPFP thyroid cancer. However, only limited data exist to characterize the binding sites and oncogenic function of PPFP, or to explain the observed therapeutic effect of pioglitazone. Here we used our previously characterized transgenic mouse model of PPFP follicular thyroid carcinoma to identify PPFP binding sites in vivo using ChIP-seq, and to distinguish genes and pathways regulated directly or indirectly by PPFP with and without pioglitazone treatment via integration with RNA-seq data. PPFP bound to DNA regions containing the PAX8 and/or the PPARG motif, near genes involved in lipid metabolism, the cell cycle, apoptosis, and cell motility; the binding site distribution was highly concordant with our previous study in a rat PCCL3 cell line. Most strikingly, pioglitazone induced an immune cell infiltration including macrophages and T cells only in the presence of PPFP, which may be central to its therapeutic effect.
2016-12-21 | GSE85648 | GEO
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
Project description:Genomic binding and regulation of gene expression by the thyroid carcinoma-associated PAX8-PPARG fusion protein
| PRJNA288400 | ENA
Project description:In order to define the transcriptional network functionally regulated by Pax8 as well as infer its direct targets, we performed RNAi to knock-down Pax8 gene in FRTL-5 thyroid cells. Expression data from three independent silencing experiments were analyzed by microarray technology unraveling 2815 genes differentially expressed between silenced cells and controls. Of these, 1421 genes were down-regulated and 1394 genes were up-regulated 72hrs after Pax8 silencing. The results obtained suggest that Pax8 regulates numerous pathways, some of which involved in the regulation of cell cycle, thyroid cancer and apoptosis, thus confirming that Pax8 is a master regulatory gene. Rat differentiated thyroid cells from FRTL-5 line were transfected with siGENOME Pax8 siRNA (siPax8, experimental) or siGENOME Non-Targeting siRNA (ntPax8, controls). The trascriptome from three siPax8 biological replicates, 72 hours after transfection, was compared to the trascriptome from 3 control ntPax8 biological replicates. Microarray analysis was performed at gene-level using the AffymetrixGeneChip Rat Gene 1.0 ST array
2011-12-20 | E-GEOD-29341 | biostudies-arrayexpress
Project description:In order to define the transcriptional network functionally regulated by Pax8 as well as infer its direct targets, we performed RNAi to knock-down Pax8 gene in FRTL-5 thyroid cells. Expression data from three independent silencing experiments were analyzed by microarray technology unraveling 2815 genes differentially expressed between silenced cells and controls. Of these, 1421 genes were down-regulated and 1394 genes were up-regulated 72hrs after Pax8 silencing. The results obtained suggest that Pax8 regulates numerous pathways, some of which involved in the regulation of cell cycle, thyroid cancer and apoptosis, thus confirming that Pax8 is a master regulatory gene.
2011-12-20 | GSE29341 | GEO
Project description:Although fine needle aspiration (FNA) cytology is helpful in determining whether thyroid nodules are benign or malignant, this distinction remains challenging in follicular neoplasms. Identification of genomic alterations in cytological specimens that distinguish between benign and malignant follicular tumors would have great clinical value. This study identified chromosomal imbalances in a set of 126 thyroid frozen follicular lesions characterized by histopathology, using aCGH, FISH, and DNA ploidy determination. An evaluation algorithm was developed based on a panel of three FISH experiments to better distinguish between follicular adenomas and carcinomas of the thyroid. This algorithm detects structural abnormalities that were observed in about half of the follicular thyroid carcinomas. These molecular markers may be therefore useful as an adjunct for making a differential diagnosis of follicular adenoma versus follicular carcinoma using cytological material obtained by FNA. Further information on the values in the comment columns: [FISH_1p_Loss : Status for abnormality found in terms of copy number variation for chr1p by FISH], [FISH_22_Loss : Status for abnormality found in terms of copy number variation for chr22 by FISH], [FISH_X_Gain : Status for abnormality found in terms of copy number variation for chrX by FISH], [FISH_Global : Status for abnormality found in terms of copy number variation for at least one of these (chr1p, chr22, chrX) by FISH], [DNA_Index : Measured by flow cytometry], [KRAS_Mutation : Mutation status for KRAS, obtained from Sanger sequencing. wt for wild-type, mut for mutant], [HRAS_Mutation : Mutation status for HRAS, obtained from Sanger sequencing. wt for wild-type, mut for mutant], [NRAS_Mutation : Mutation status for NRAS, obtained from Sanger sequencing. wt for wild-type, mut for mutant], [BRAF_Mutation : Mutation status for BRAF, obtained from Sanger sequencing. wt for wild-type, mut for mutant], [CTNNB1_Mutation : Mutation status for CTNNB1, obtained from Sanger sequencing. wt for wild-type, mut for mutant], [PIK3CA_Mutation : Mutation status for PIK3CA, obtained from Sanger sequencing. wt for wild-type, mut for mutant], [PAX8-PPARg_Fusion : Status for the PAX8-PPARG gene fusion, obtained from qRT-PCR. pos for presence of fusion, neg for absence], [RET-PTC_Fusion : Status for the RET-PTC gene fusion, obtained from qRT-PCR. pos for presence of fusion, neg for absence], [Mutation_Status : Global mutation status, combining results from HRAS, NRAS mutation status, and PAX8-PPARG fusion status], [Tumor_Size_cm : Tumor size in centimeters], [pT : Classes defined according to the size of the tumors (for more information, check AJCC classification)], [pN : Classes defined according to the number of nodes involved or not (for more information, check AJCC classification)], [pM : Classes defined according to the presence or absence of distant metastases (for more information, check AJCC classification)], [Carcinoma_Histo_Type : Histological type for carcinoma. MIF for minimally invasive, WIF for widely invasive], [Adenoma_Histo_Type : Histological type for adenoma. MIC for microvesicular, MAC for macrovesicular, BOTH for both], [Follow-up_month : Patient follow-up in months], [Alive_status : Patient alive status. yes for alive patient, no for deceased patient], [Metastasis_status : Presence of metastasis during the follow-up. yes for positive, no for negative, possible when uncertainty remains].
2013-07-01 | E-MTAB-1575 | biostudies-arrayexpress