Proteogenomics analysis unveils a TFG-RET gene fusion and druggable targets in papillary thyroid carcinomas
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ABSTRACT:
PROVIDER: PRJEB37220 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4008067_1.fastq.gz | Fastqsanger.gz | |||
| ERR4008067_2.fastq.gz | Fastqsanger.gz | |||
| ERR4008068_1.fastq.gz | Fastqsanger.gz | |||
| ERR4008068_2.fastq.gz | Fastqsanger.gz | |||
| ERR4008069_1.fastq.gz | Fastqsanger.gz |
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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
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
Project description:Papillary thyroid cancer (PTC) is the most common type of endocrine malignancy. By RNA-seq analysis, we identify a RET rearrangement in the tumour material of a patient who does not harbour any known RAS or BRAF mutations. This new gene fusion involves 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. TFG-RET oligomerises in a PB1 domain-dependent manner and oligomerisation of TFG-RET is required for oncogenic transformation. Quantitative proteomic analysis reveals the upregulation of E3 Ubiquitin ligase HUWE1 and DUBs like USP9X and UBP7 in both tumor and metastatic lesions, which is further confirmed in additional patients. Expression of TFG-RET leads to the upregulation of HUWE1 and inhibition of HUWE1 significantly reduces RET-mediated oncogenesis.
| S-EPMC7188865 | biostudies-literature
Project description:Genomic rearrangements leading to intragenic gene fusion are mainly found in some types of haematopoietic malignancies and sarcomas. Recently they have been described also in carcinomas such as the papillary thyroid histotype (60%-70%) and the Hürthle thyroid tumours (58%). The presence of junction oncogene constitutes an area of exciting research for emerging therapy as targeting the RET-PTC1 fusion oncogene by using small interfering RNA (siRNA) strategies since it is present only in the tumour cells and not in the surrounding normal cells. Therefore, we developed a siRNA against RET-PTC1 junction and assess its efficiency on the human papillary thyroid carcinoma cell line TPC-1 which spontaneously harbours the RET-PTC1 oncogene. The targeted genes are assessed by microarray analysis by comparing the regulated genes by the siRNA_RET-PTC1 vs a siRNA_RET developed on the RET part of the mRNA minus the siRNA_control that contain four mutation within the RET-PTC1 sequence. To test the targeted genes in the TPC-1 cell line that spontaneously harbours RET-PTC1 junction of two siRNAs developed: Within the RET-PTC1 junction, and in the mRNA RET part. A non-specific siRNA harbouring 4 mutations within the RET-PTC1 sequence was used as negative control (siRNA_control). By real-time PCR (Q-RT-PCR) we demonstrated that both siRNAs (siRNA_RET-PTC1 and siRNA_RET) significantly reduce RET mRNA levels of about 85 % in TPC-1 cells. The negative control did not show an effect of RET mRNA levels. Three independent transfections were performed on TPC-1 cells using 5 µl of Lipofectamine 2000 transfection reagent (Invitrogen, Cergy-Pontoise, France) and 50nM of i) siRNA_RET-PTC1 or ii) siRNA_RET or iii) siRNA_control that harbour 4 mutations within its sequence. Total RNAs of untreated cells and transfected cells were purified using the RNA cleanup and concentration kit (QIAGEN, Hilden, Germany) and gathered in 4 pools : 1) TPC-1 harbouring RET-PTC1 ; 2) TPC-1 silenced for RET-PTC1 with siRNA RET-PTC1 ; 3) TPC-1 silenced for siRNA RET ; 4) TPC-1 treated with the siRNA control.
2010-05-01 | E-TABM-746 | biostudies-arrayexpress
Project description:RET fusions (e.g., with KIF5B, CCDC6, and NCOA4) drive subsets of non-small cell lung cancer (NSCLC) and papillary thyroid carcinoma (PTC). Despite improvements in precision therapy using selective RET tyrosine kinase inhibitors (TKIs), resistance occurs and is often driven by RET-independent bypass mechanisms. SRC is a non-receptor tyrosine kinase and a well-known oncogene promoting proliferation, migration, stemness, etc. Although previous studies have implied crosstalk between RET and SRC, the anti-cancer effects of targeting SRC combined with first line RETi treatment, and their related molecular mechanisms are still not fully elucidated. Thus, we aimed to determine whether SRC inhibition enhances the anti-cancer effects of RET TKIs to create a combination strategy to treat RET fusion-positive (RET+) NSCLC and PTC. Our results showed that the SRC TKI, dasatinib, significantly enhanced the anti-cancer activities of RET TKIs in vitro. From phosphoproteomics analysis and validation assays using selective inhibitors and siRNAs, we have defined that dasatinib synergizes with RET TKIs through further suppression of PAK, AKT and S6 signaling pathways. Moreover, rescue experiments using SRC gatekeeper mutation (T341I) further validated that the combination effects between RET TKIs and dasatinib were SRC-dependent. Importantly, we also observed synergistic effects in RET+ cancer cells between RET TKIs and eCF506, a next-generation clinical SRC inhibitor with higher selectivity. Finally, both dasatinib and scF506 could restore selpercatinib sensitivity in a selpercatinib-resistant RET+ PTC cell line. Altogether, our results suggest that SRC and RET signaling crosstalk to activate RET canonical and non-canonical downstream pathways in RET+ NSCLC and PTC and that SRC inhibition has clinical potential against TKI-naïve and -resistant RET+ cancers.The experimental design for the tandem mass tag labeling was: DMSO (126, 127CC, 128C), DMSO 24 hrs. (127N, 128N, 129N), Pralsetinib 3 hrs. (129C, 130C, 131C), Pralsetinib 24 hrs. (130N, 131N, 132N), Dasatinib 3 hrs. (132C, 133C, 134C), PralDasa Combination 3 hrs. (133N, 134N, 135N). In the filenames, ID indicates expression proteomics; IMAC indicates phosphoproteomics.
2025-10-22 | PXD063113 | Pride
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
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. miRNA expression profiles of thyrocytes expressing RET/PTC1 oncogene and parental thyrocytes were compared. Biological replicates could not be generated.
2014-06-30 | E-GEOD-49400 | biostudies-arrayexpress
Project description:BLU667-adapted transcriptome in CCDC6-RET fusion papillary thyroid carcinoma (TPC) cells
| PRJNA870058 | ENA
Project description:transcriptome comparison of radiation-induced papillary thyroid carcinomas with sporadic papillary thyroid carcinomas
2005-10-27 | E-MEXP-485 | biostudies-arrayexpress
Project description:To investigate the short-termed and long-termed transcriptomic changes induced by the RET tyrosine kinase inhibitor BLU667 in TPC-1 human PTC cells
2023-04-11 | GSE211371 | GEO