Similar Datasets
Project description:Paillary thyroid cancer (PTC) is the most common type of thyroid malignancy. Extrathyroidal invasion (ETİ), lymph node metastasis, and distance organ metastasis is poor prognostic factor in PTC. The metastasis is still a leading cause of papillary thyroid cancer death. The early detection of metastatic signature is crucial for identification of thyroid cancer prognosis and personalized therapeutic strategies. In the present study, we present thyroid cancer metastasis and invasivenes related miRNAs identified by comprehensive miRNA expression profiling of formalin-fixed paraffin embedded (FFPE) thyroid tissues obtained from patients belonging to intrathyroidal, invasive and metastatic thyroid carcinoma groups
2020-03-23 | GSE129878 | GEO
Project description:Paillary thyroid cancer (PTC) is the most common type of thyroid malignancy. Extrathyroidal invasion (ETİ), lymph node metastasis, and distance organ metastasis is poor prognostic factor in PTC. The metastasis is still a leading cause of papillary thyroid cancer death. The early detection of metastatic signature is crucial for identification of thyroid cancer prognosis and personalized therapeutic strategies. In the present study, we present thyroid cancer metastasis and invasivenes related miRNAs identified by comprehensive miRNA expression profiling of formalin-fixed paraffin embedded (FFPE) thyroid tissues obtained from patients belonging to intrathyroidal, invasive and metastatic thyroid carcinoma groups
2020-03-23 | GSE129879 | GEO
Project description:miRNA expression profiles in non-aggressive, invasive and metastatic papillary thyroid cancer
| PRJNA533088 | ENA
Project description:miRNA and mRNA expression profiles in non-aggressive, invasive and metastatic papillary thyroid cancer
| PRJNA533087 | ENA
Project description:mRNA expression profiles in non-aggressive, invasive and metastatic papillary thyroid cancer
| PRJNA533089 | ENA
Project description:Papillary thyroid cancer (PTC) can be divided into classical variant of PTC (cPTC), follicular variant of PTC (fvPTC), and tall cell variant (tcPTC). These variants differ in their histopathology and cytology; however, their molecular background is not clearly understood. Our results shed some new light on papillary thyroid cancer biology as new direct miRNA-gene regulations are discovered. The Cancer Genome Atlas (TCGA) 466 thyroid cancer samples were studied in parallel datasets to discover potential miRNA-mRNA regulations. Additionally, miRNAs and genes differentiating PTC variants (cPTC, fvPTC, and tcPTC) were indicated. Putative miRNA regulatory pairs were discovered: hsa-miR-146b-5p with PHKB and IRAK1, hsa-miR-874-3p with ITGB4 characteristic for classic PTC samples, and hsa-miR-152-3p with TGFA characteristic for follicular variant PTC samples. MiRNA-mRNA regulations discovery opens a new perspective in understanding of PTC biology. Furthermore, our successful pipeline of miRNA-mRNA regulatory pathways discovery could serve as a universal tool to find new miRNA-mRNA regulations, also in different datasets.
| S-EPMC5021476 | biostudies-literature
Project description:Aggressive variants of papillary thyroid carcinoma (PTC) have been described with increasing frequency and are associated with unfavorable clinical outcomes. However, limited data exist on the comprehensive genetic profile of these variants. We performed targeted next-generation sequencing in 36 patients with aggressive variants of PTC and compared it to PTC from The Cancer Genome Atlas (TCGA) project and poorly differentiated thyroid cancers (PDTCs)/anaplastic thyroid cancers (ATCs) from the Memorial Sloan Kettering Cancer Center (MSKCC). BRAF mutation was the most prevalent (89%) in aggressive variants of PTC compared to that in other thyroid cancers. RAS mutation was identified in one patient (3%), which was less frequent than in others. TERT promoter mutation (17%) ranged between that of PTCs (9%) and PDTCs (40%). Tumor suppressor genes, ZFHX3, TP53, and CHEK2, were mutated in 14%, 3%, and 6% of aggressive variants of PTC, respectively. The mutation rate of TP53 (3%) was significantly higher than that of PTCs (0.7%) and lower than that of ATCs (73%). Mutations in three functional groups, histone methyl transferases, SWI/SNF chromatin remodeling complex, and the PI3K/AKT/mTOR pathway, were present in 11%, 14%, and 11% of samples, respectively. In conclusion, aggressive variants of PTC had higher BRAF and lower NRAS mutation prevalence than other thyroid cancers. The prevalence of mutations in the TERT promoter, TP53, and genes encoding three functional groups ranged between that of PTCs and PDTCs/ATCs.
| S-EPMC7924361 | biostudies-literature
Project description:BackgroundPapillary thyroid cancer (PTC) is the most frequent endocrine tumor. Radioiodine (RAI) treatment is highly effective in these tumors, but up to 60% of metastatic cases become RAI-refractory. Scanty data are available on either the molecular pattern of radioiodine refractory papillary thyroid cancers (PTC) or the mechanisms responsible for RAI resistance.MethodsWe analyzed the molecular profile and gene/miRNA expression in primary PTCs, synchronous and RAI-refractory lymph node metastases (LNMs) in correlation to RAI avidity or refractoriness. We classified patients as RAI+/D+ (RAI uptake/disease persistence), RAI-/D+ (absent RAI uptake/disease persistence), and RAI+/D- (RAI uptake/disease remission), and analyzed the molecular and gene/miRNA profiles, and the expression of thyroid differentiation (TD) related genes.ResultsA different molecular profile according to the RAI class was observed: BRAFV600E cases were more frequent in RAI-/D+ (P = 0.032), and fusion genes in RAI+/D+ cases. RAI+/D- patients were less frequently pTERT mutations positive, and more frequently wild type for the tested mutations/fusions. Expression profiles clearly distinguished PTC from normal thyroid. On the other hand, in refractory cases (RAI+/D+ and RAI-/D+) no distinctive PTC expression patterns were associated with either tissue type, or RAI uptake, but with the driving lesion and BRAF-/RAS-like subtype. Primary tumors and RAI-refractory LNMs with BRAFV600E mutation display transcriptome similarity suggesting that RAI minimally affects the expression profiles of RAI-refractory metastases. Molecular profiles associated with the expression of TPO, SLC26A4 and TD genes, that were found more downregulated in BRAFV600E than in gene fusions tumors.ConclusionsThe present data indicate a different molecular profile in RAI-avid and RAI-refractory metastatic PTCs. Moreover, BRAFV600E tumors displayed reduced differentiation and intrinsic RAI refractoriness, while PTCs with fusion oncogenes are RAI-avid but persistent, suggesting different oncogene-driven mechanisms leading to RAI refractoriness.
| S-EPMC7667839 | biostudies-literature
Project description:The current focus in the treatment of papillary thyroid carcinoma (PTC) is tumor progression. The aim of this study was to build RNA-based classifiers and develop a comprehensive model to provide progression-free interval (PFI) risk prediction for PTC. The RNAseq data, miRNAseq data, and clinical information of PTC were downloaded from The Cancer Genome Atlas database. Based on the differently expressed RNAs, the least absolute shrinkage and selection operator (LASSO) Cox regression model was utilized to build the RNA-based classifiers for PFI of the patients with PTC. A 6-messenger RNA (mRNA)-based classifier, a 5-long non-coding RNA (lncRNA)-based classifier, and a 4-microRNA (miRNA)-based classifier were constructed to predict the PFI. Patients with high risk based on the constructed RNA-based classifiers had worse prognosis in Kaplan-Meier curve analysis with log-rank test. The areas under the curves of the first, third, and fifth years in the training and testing set were 0.83, 0.82, and 0.82 and 0.67, 0.72, and 0.73 for the 6-mRNA-based classifier, respectively; 0.75, 0.84, and 0.85 and 0.71, 0.67, and 0.71 for the 5-lncRNA-based classifier, respectively; and 0.70, 0.77, and 0.79 and 0.74, 0.67, and 0.66 for the 4-miRNA-based classifier, respectively. The prediction capability of the three RNA-based classifiers was superior to the TNM stage system. Furthermore, a nomogram based on the verified independent prognostic factors was established for the prognostic prediction. The C-index and calibration plots indicated good predictive accuracy of the nomogram. In summary, the 6-mRNA-based classifier and 5-lncRNA-based classifier constructed in this study were independent prognostic factors for PTC.
| S-EPMC7417634 | biostudies-literature
Project description:Accumulating evidence has indicated that long noncoding RNAs (lncRNAs) are the main constituents of competing endogenous RNA (ceRNA) networks. Nonetheless, in the lncRNA-related ceRNA network of papillary thyroid cancer (PTC), the function of cancer-specific lncRNAs, as well as their use for the potential prediction of PTC prognosis, remains unclear. In this study, 384 RNA sequencing (RNA-seq) profiles of PTC patients were attained from The Cancer Genome Atlas (TCGA), an open-source database that offers vast amounts of RNA-seq data, and 75 miRNAs, 495 lncRNAs, and 1099 mRNAs (P < .05 and |logFC| >2) were detected when compared with normal tissues. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed using the Cytoscape plug-in BinGo. An aberrant lncRNA-mRNA-miRNA ceRNA network consisting of 31 differentially expressed (DE)-lncRNAs, 13 DE-miRNAs, and 134 DE-mRNAs was built in TCGA. On the basis of overall survival (OS) analysis, 6 lncRNAs (CCAT1, SYNPR, SFTA1P, HOTAIR, HCG22, and CLDN10) were identified as prognostic biomarkers for patients in TCGA (P < .05). Through qRT-PCR, we designated 6 cancer-specific lncRNAs as having great significance for survival by verifying their expression in the 60 PTC patients who were diagnosed. The qRT-PCR and TCGA results were completely consistent. Our research provides data for further understanding the lncRNA-miRNA-mRNA ceRNA network and elucidating the molecular mechanisms of PTC.
| S-EPMC7647549 | biostudies-literature