Hsa-miR-199a-3p is an oncosuppressor microRNA in papillary thyroid carcinoma
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Matteo Dugo
PROVIDER: E-GEOD-49415 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-03-31 | E-GEOD-59595 | biostudies-arrayexpress
Project description:Gene and miRNA profiles from a unique Chinese/Caucasian trans-ethnic collection of breast cancer from Shanghai (China) and Milan (Italy) were compared using an unsupervised approach that identified similar clusters of correlated features in Chinese and Caucasian datasets. Partition of gene expression data using previously published gene signatures, such as the PAM50 intrinsic gene list and the extracellular matrix (ECM) genes, revealed Chinese and Caucasian subgroups with equivalent gene and miRNA expression profiles. A significant reduction of Luminal-A tumors was observed in the Chinese series. Tissue samples from 78 Chinese (Han Chinese) and 97 Italian (South Europe Caucasian) consecutive primary breast tumors were subjected to gene and miRNA profiling. Tissue specimens, initially collected respectively in the Chinese and Italian hospitals, were all stored, randomly processed and analyzed in identical experimental conditions in the Italian center to minimize pre-analytical, instrumental and computational variability, enabling direct comparison of gene and miRNA profiles from the two groups.
2015-03-31 | E-GEOD-59594 | biostudies-arrayexpress
Project description:We treated the papillary thyroid carcinoma-derived cell line TPC1 with the RTK inhibitor RPI-1 to obtain a thyroid carcinoma cell model. The RET tyrosine kinase is a target of the inhibitor. microRNA expression changes were evaluated comparing cells treated with the inhibitor fo 24 hours versus cells treated with DMSO for 24 hours. Biological triplicates for RPI-1 and DMSO treated cells were generated by independent treatments and total RNA extractions. One sample from each class did not pass quality control, and thus was discarded. The final dataset comprises two samples for each class.
2014-06-30 | E-GEOD-49401 | biostudies-arrayexpress
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:We treated the papillary thyroid carcinoma-derived cell line TPC1 with the RTK inhibitor RPI-1 to obtain a thyroid carcinoma cell model. The RET tyrosine kinase is a target of the inhibitor. Gene expression changes were evaluated comparing cells treated with the inhibitor for 24 hours versus cells treated with DMSO for 24 hours. Biological triplicates for RPI-1 and DMSO treated cells were generated by independent treatments and total RNA extractions.
2014-06-30 | E-GEOD-49414 | biostudies-arrayexpress
Project description:Whole transcriptome Identification of direct targets of miR-199a-5p and miR-424-3p using biotinylated pull-downs found that both miRNAs are likely to have a role in the cell cycle. HEK293T cells were transfected with biotinylated miRNAs (either miR-199a-5p or miR-424-3p). The miRNAs and target mRNA were pulled down with streptavidin and compared to the input control.
2013-12-02 | E-GEOD-40406 | biostudies-arrayexpress
Project description:Gene and miRNA profiles from a unique Chinese/Caucasian trans-ethnic collection of breast cancer from Shanghai (China) and Milan (Italy) were compared using an unsupervised approach that identified similar clusters of correlated features in Chinese and Caucasian datasets. Partition of gene expression data using previously published gene signatures, such as the PAM50 intrinsic gene list and the extracellular matrix (ECM) genes, revealed Chinese and Caucasian subgroups with equivalent gene and miRNA expression profiles. A significant reduction of Luminal-A tumors was observed in the Chinese series. Tissue samples from 78 Chinese (Han Chinese) and 97 Italian (South Europe Caucasian) consecutive primary breast tumors were subjected to gene and miRNA profiling. Tissue specimens, initially collected respectively in the Chinese and Italian hospitals, were all stored, randomly processed and analyzed in identical experimental conditions in the Italian center to minimize pre-analytical, instrumental and computational variability, enabling direct comparison of gene and miRNA profiles from the two groups.
2015-03-31 | E-GEOD-59590 | biostudies-arrayexpress
Project description:The function of human circulating proangiogenic cells (PACs) has been described extensively. However, little focus has been placed on understanding how these cells differ in their functions in the presence of microenvironments mimicking vascular inflammation. We hypothesized that exposure to proinflammatory cytokines or the oxLDL, an autoantigen abundant in advanced atherosclerotic plaques, converts PACs into immune-modulating/proinflammatory cells. Hence, we examined the effect of oxLDL and inflammatory stimuli on their phenotype by use of a functional genomics model based on secretome and whole genome transcriptome profiling. PACs obtained from culturing a PBMC fraction in angiogenic medium were primed with DC differentiation cytokines for 3 days and then exposed to proinflammatory cytokines or oxLDL for 2 days. Under these conditions, PACs converted into APCs (APCcy and APCox, respectively), expressed maturation markers CD80 and CD83, and showed an up-regulation of CD86. APCcy and APCox induced a robust T cell BrdU incorporation. Despite a similar ability to induce lymphocyte proliferation, APCcy and APCox differed for the secretory pathway and mRNA expression. Analysis of the differentially expressed genes identified 4 gene "clusters", showing reciprocal modulation in APCcy vs. APCox justifying, according to functional genomics analyses, a different putative function of the cells in antigen processing. Together, these data show that treatment with inflammatory cytokines or oxLDL converts human PAC phenotype and function into that of APCs with similar lymphocyte-activating ability but distinct maturation degree and paracrine functions. PBMC-derived PACs were committed with GM-CSF and IL-4 to a dendritic phenotype, and then exposed to proinflammatory cytokines (IL-1β and TNF-α) or to the oxidized form of LDL (oxLDL). Functional assays and whole genome gene expression profiling were performed both on PACs (n=6) and or resulting cytokine- (APCcy, n=6) and oxLDL-induced APCs (APCox, n=6). RNA was reverse transcribed, labeled, and linearly amplified, and then hybridized to HumanHT-12 v.4 Expression BeadChip microarrays. To estimate technical variability, ≈20% of the samples (n=4) were hybridized in duplicate.
2015-06-30 | E-GEOD-60208 | biostudies-arrayexpress
Project description:Osteopontin (OPN) is a secreted glycoprotein, belonging to the non-structural extracellular matrix (ECM), and its over expression in human prostate cancer cells has been associated with disease progression, androgen independence and metastases. Nevertheless the pathophysiology of OPN in prostate tumorigenesis has never been studied. We crossed TRansgenic Adenocarcinoma of the Mouse Prostate (TRAMP) mice with OPN deficient (OPN-/-) mice and followed tumor onset and progression in these double mutants. Ultrasound examination detected the early onset of a spherical homogeneous tumor in about 60% of OPN-/- TRAMP mice that seldom occurs in parental TRAMP mice. Histology and immunohistochemistry characterized these tumors for being Tag positive but negative for AR, highly proliferative and endowed of neuroendocrine (NE) features. Gene expression profiling showed up-regulation of genes involved in tumor progression, cell cycle and neuronal differentiation in OPN-deficient versus -sufficient TRAMP tumors. Down-regulated genes included key genes of TGFï?¢ pathway, and a role for TGFï?¢ in NE differentiation of prostate cancer was also confirmed at the protein level. Furthermore, NE genes and particularly those characterizing early prostatic lesions of OPN-deficient mice were found to correlate with those of human NE tumours. These data underscore a novel role of OPN at early stages of prostate cancer growth, protecting against the development of aggressive NE tumors. Total RNA obtained from prostate tumors from 18 and 30 weeks old TRAMP mice, compared to RNA extracted from prostate tumors and prostate tissue from Osteopontin-deleted TRAMP mice
2016-01-20 | E-GEOD-69903 | biostudies-arrayexpress
Project description:miRNA expression profiles were evaluated in a series of 64 prostate clinical specimens, including 32 cancer and 32 non-neoplastic tissues. For 26 individuals, paired cancer and non-neplastic tissue was available. Tumor and non-neoplastic tissues were obtained, with appropriate informed consent and Institutional Review Board approval, from untreated prostate cancer patients subjected to radical prostatectomy. Freshly frozen surgical blocks were carefully dissected by the pathologist using H&E-stained sections as a template to identify areas containing at least 70% of tumor or normal cells. The total series comprises 64 clinical specimens, of which 32 from cancer areas and 32 from benign areas. For 26 patients, matched tumor and normal samples were available.
2015-12-23 | E-GEOD-76260 | biostudies-arrayexpress