Identification of miRNAs regulated by TGF-b in human CD8+ T cells (expression)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Anoop Chandran P
PROVIDER: E-GEOD-46324 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The goal of the current study was to identify miRNAs regulated by TGF-b in human CD8+ T cells and analyze the function of these miRNAs in shaping the immunomodulatory effect of TGF-b in these cells. We identified the miR-23a cluster to be upregulated and found that this cluster could target key molecules (IFN-g and LAMP1) involved in immune response by CD8+ T cells. CD8+ T cells were isolated and purified from healthy human peripheral blood of 5 donors and were activated using beads coupled to anti-CD2, anti-CD3 and anti-CD24. They were then treated with 5ng/ml TGF-b, with 1µM SD-208 or left untreated. RNA from these cells were then isolated and used for deep sequencing.
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2013-09-05 | E-GEOD-40587 | biostudies-arrayexpress
Project description:The goal of the current study was to identify miRNAs regulated by TGF-b in human CD8+ T cells and analyze the function of these miRNAs in shaping the immunomodulatory effect of TGF-b in these cells. We identified the miR-23a cluster to be upregulated and found that this cluster could target key molecules (IFN-g and LAMP1) involved in immune response by CD8+ T cells.
2014-08-01 | GSE46324 | GEO
Project description:The goal of the current study was to identify miRNAs regulated by TGF-b in human CD8+ T cells and analyze the function of these miRNAs in shaping the immunomodulatory effect of TGF-b in these cells. We identified the miR-23a cluster to be upregulated and found that this cluster could target key molecules (IFN-g and LAMP1) involved in immune response by CD8+ T cells.
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Project description:MicroRNAs (miRNAs) are small non-coding RNAs that associate with Argonaute 2 protein to regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent studies have reported that some miRNAs localize to and function in other cellular compartments. Mitochondria harbour their own genetic system that may be a potential site for miRNA-mediated post-transcriptional regulation. We aimed at investigating whether nuclear-encoded miRNAs can localize to and function in human mitochondria. To enable identification of mitochondrial-enriched miRNAs, we profiled the mitochondrial and cytosolic RNA fractions from the same HeLa cells by miRNA microarray analysis. Mitochondria were purified using a combination of cell fractionation and immunoisolation, and assessed for the lack of protein and RNA contaminants. We found 57 miRNAs differentially expressed in HeLa mitochondria and cytosol. Of these 57, a signature of 13 nuclear-encoded miRNAs was reproducibly enriched in mitochondrial RNA and validated by RT-PCR for hsa-miR-494, hsa-miR-1275 and hsa-miR-1974. This study provides the first comprehensive view of the localization of RNA interference components to the mitochondria. Our data outline the molecular bases for a novel layer of crosstalk between nucleus and mitochondria through a specific subset of human miRNAs that we termed ‘mitomiRs’. To assess whether nuclear-encoded miRNA are detectable in human mitochondria, we performed the following four steps approach. First, cultured HeLa cells were allowed to reach 80-100% confluence and subjected to fractionation in order to isolate the cytosolic fraction. From the same HeLa cells, mitochondria were isolated by immunomagnetic Anti-TOM22 MicroBeads from the Mitochondria Isolation Kit (Miltenyi Biotec). In total, six mitochondria preparations were perfromed, three of these were additionally treated with RNase A. Second, total RNA was extracted from the mitochondrial and cytosolic fractions. Third, mitochondrial and cytosolic RNA were respectively profiled by microRNA microarray analysis. Last, data were analyzed and normalized.Three independent assays were performed.
2011-10-05 | E-GEOD-24761 | biostudies-arrayexpress
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2015-04-14 | E-GEOD-55530 | biostudies-arrayexpress
Project description:MicroRNAs are small, non-coding RNAs that regulate gene expression at post-transcriptional levels. There is increasing evidence to suggest that miRNAs could be useful in cancer diagnosis, prognosis, and therapy. The aim of our study was to identify miRNAs predictors of poor prognosis in adrenocortical cancer. miRNA microarray expression profiling was performed on a cohort of 6 adenomas, 6 non-recurrent carcinomas (Carc_B) and 6 recurrent carcinomas (Carc_A). We identified several miRNAs that were differentially expressed between adenomas and carcinomas as well as between Carc_A and Carc_B. We found that the best discriminatory miRNAs between carcinomas and adenomas were miR-195 and miR-335 which were down-regulated in carcinomas. MiR-139-5p was the most powerful discriminatory miRNA between Carc_A and Carc_B subtypes with consistent up-regulation in the recurrent carcinoma subgroup (Carc_A). Target prediction analysis showed that predicted targets of these miRNAs could be involved in biological processes and pathways that enhance tumor progression. Our data suggest that adrenocortical cancer cells progressively switch from a high miR-195 and miR-335 status to a low miR-195 and miR-335 phenotype. MiR-139-5P is a potential prognostic biomarker of recurrent adrenocortical carcinomas. Six tumor samples from patients with adrenocortical adenomas (Adenoma_1 to Adenoma_6), six tumor samples from patients with aggressive carcinomas (Carc_A1 to Carc_A6) and six tumor samples from patients with non-aggressive carcinoma (Carc_B1 to Carc_B6) were used to prepare total RNA for microarray analysis using MiRXploreTM Microarrays. miRXplore Universal Reference was used as control. One tumor sample was used per array.
2013-06-30 | E-GEOD-43279 | biostudies-arrayexpress
Project description:BACKGROUND: Orofacial development is a multifaceted process involving precise, spatio-temporal expression of a panoply of genes. MicroRNAs (miRNAs) constitute the largest family of noncoding RNAs involved in gene silencing, and represent critical regulators of cell and tissue differentiation. MicroRNA gene expression profiling is an effective means of acquiring novel and valuable information regarding the expression and regulation of genes, under the control of miRNA, involved in mammalian orofacial development. RESULTS: To identify differentially expressed miRNAs during mammalian orofacial ontogenesis, miRNA expression profiles from gestation day (GD) -12, -13 and -14 murine orofacial tissue were compared utilizing miRXplore™ microarrays from Miltenyi Biotech GmbH. TaqManTM quantitative Real-Time PCR was utilized for validation of gene expression changes. Cluster analysis of the microarray data was conducted with the clValid R package and the UPGMA (hierarchical) clustering method. Functional relationships between selected miRNAs were investigated using Ingenuity Pathway Analysis. Expression of over 26% of the approximately 588 murine miRNA genes examined was detected in murine orofacial tissues from GD 12, 13 and 14. Among these expressed genes several clusters were seen to be developmentally regulated. Differential expression of genes encoding miRNAs within such clusters were shown to target genes encoding proteins involved in cell proliferation, cell adhesion, differentiation, apoptosis and epithelial-mesenchymal transformation, all processes critical for normal orofacial development. Functional relationships between miRNAs differentially expressed were investigated using Ingenuity Pathway Analysis (IPA; Ingenuity Systems). CONCLUSIONS: Using miRNA microarray technology, unique gene expression signatures of hundreds of miRNAs in embryonic orofacial tissue were defined. Gene targeting and functional analysis revealed that the expression of numerous protein-encoding genes, crucial to normal orofacial ontogeny, may be regulated by specific miRNAs. Time-course experiment (Developmental Stages), ICR mice embryos on gestational days (GD) 12, 13 and 14. Biological replicates: For each day of gestation, 3 independent pools of 15 to 20 staged embryos were used to procure embryonic orofacial tissues for preparation of 3 distinct pools of RNA that were independently processed and applied to individual miRXplore™ microRNA Microarray chips (Miltenyi Biotec GmbH). Technology: 2-color spotted cDNA, Hy5 (experimental sample) vs. Hy3 (control - miRXplore Universal Reference).
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