Circular RNA cFUT8 acts as an epithelial–mesenchymal transition trigger in liver cancer.
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE78520 | GEO | 2016/02/26
SECONDARY ACCESSION(S): PRJNA313205
REPOSITORIES: GEO
Similar Datasets
Project description:Using the highly sensitive cricRNA array, we screened 13617 circRNAs abundant in the human liver cancer and Adjacent normal liver tissues, and the function of differentially expressed circRANs were analyzed by bioinformatics. The results revealed that cFUT8 controls epithelialâmesenchymal transition in liver cancer by cFUT8/miR-548c-3p/FUT8 axis. In this study, three cases of liver cancer samples were used to acquire the circRNA expression profiling, and qRT-PCR was employed to confirm the results of circRNA microarrays. The functions of the differentially expressed circRNA were analyzed by bioinformatics methods. Finally, through in vivo and ex vivo experimentsï¼the âcFUT8/miR-548c-3p/FUT8 axisâ was found to control epithelialâmesenchymal transition in liver cancer
2016-02-26 | E-GEOD-78520 | biostudies-arrayexpress
Project description:Background: circRNAs, a recently identified new member of non-coding RNAs, have been proved to play an essential role in the development and progression of various cancers. However, the functions and mechanisms of circRNAs in colorectal liver metastasis have not been fully elucidated. Methods: We performed circRNA microarray to screen differentially expressed novel circRNAs in the pathology of colorectal liver metastasis. Quantitative real-time PCR was used to detect the circ102049 expression in colorectal cancer (CRC) samples. Then CRC cells were transfected with a circ102049 over-expression vector or siRNAs, and the effects of circ102049 on biological functions in CRC cells were accessed in vitro. Mechanistically, the bioinformatics analysis, fluorescence in situ hybridization, RIP assay, RNA pull down assay and luciferase reporter assay were conducted to confirm the relationships among circ102049, miR-761, miR-192-3p and FRAS1. Moreover, the mechanism of circ102049 how to recruit and distribute DGCR8 protein in cytoplasm was elucidated. Results: The results showed that circ102049 was highly expressed in primary CRC tumors with liver metastasis and closely correlated with the CRC patients' prognosis. Circ102049 might act as a novel metastasis-related non-coding RNA, and significantly promote the adhesion, migration and invasion abilities of CRC cells. Mechanistically, we verified that circ102049 promoted the CRC development and progression via a miR-761/miR-192-3p-FRAS1-dependent mechanism. Notably, due to the distribution of DGCR8 protein, circ102049 might also reduce the mature products of miR-761 and miR-192-3p in cytoplasm indirectly. In addition, the role of circ102049 in promoting colorectal liver metastasis was also confirmed in vivo. Conclusions: Our findings provided new clues that circ102049 might be a potential prognostic factor in CRC, and the circ102049-miR-761/miR-192-3p-FRAS1 axis could be further explored as a therapeutic target for anti-metastatic therapy in CRC patients with liver metastases. Keywords: Hsa_circ_102049, miR-761, miR-192-3p, FRAS1, Colorectal liver metastasis
2021-02-08 | GSE147597 | GEO
Project description:Background: Circular RNAs (circRNAs), a subclass of noncoding RNAs, have been reported to be involved in the progression of various diseases. However, the exact role of circRIMS1, also termed hsa_circ_0132246, in human bladder cancer remains to be discovered. Methods: By performing RNA-seq comparing bladder cell lines and normal uroepithelial cells, circRIMS1 was selected as the research object. We further verified by qRT-PCR that circRIMS1 was upregulated in bladder cancer tissue and cell lines. Proliferation, colony formation, Transwell migration, Matrigel invasion, apoptosis, western blotting and in vivo tumorigenesis and metastasis assays were utilized to evaluate the roles of circRIMS1, miR-433-3p and CCAR1. For mechanistic investigation, RNA pull-down, fluorescence in situ hybridization (FISH) and luciferase reporter assay confirmed the binding of circRIMS1 with miR-433-3p. Results: CircRIMS1 was significantly upregulated in bladder cancer and circRIMS1 expression was associated with the pathological stage and histological grade of bladder cancer. Inhibition of circRIMS1 suppressed the proliferation, migration and invasion of bladder cancer cells in vitro and in vivo, while overexpression of circRIMS1 exerted the opposite effects. Moreover, the circRIMS1/miR-433-3p/CCAR1 regulatory axis was confirmed to be responsible for the biological functions of circRIMS1. Conclusions: CircRIMS1 acts as a tumor promoter in bladder cancer to enhance tumor growth, migration and invasion via the miR-433-3p/CCAR1 regulatory axis, which provides a new therapeutic target and a novel biomarker in bladder cancer. Keywords: CircRIMS1, Bladder cancer, miR-433-3p, CCAR1, Progression, Metastasis
2020-05-09 | GSE150143 | GEO
Project description:Background: Circular RNAs (circRNAs), a subclass of noncoding RNAs, have been reported to be involved in the progression of various diseases. However, the exact role of circRIMS1, also termed hsa_circ_0132246, in human bladder cancer remains to be discovered. Methods: By performing RNA-seq comparing bladder cell lines and normal uroepithelial cells, circRIMS1 was selected as the research object. We further verified by qRT-PCR that circRIMS1 was upregulated in bladder cancer tissue and cell lines. Proliferation, colony formation, Transwell migration, Matrigel invasion, apoptosis, western blotting and in vivo tumorigenesis and metastasis assays were utilized to evaluate the roles of circRIMS1, miR-433-3p and CCAR1. For mechanistic investigation, RNA pull-down, fluorescence in situ hybridization (FISH) and luciferase reporter assay confirmed the binding of circRIMS1 with miR-433-3p. Results: CircRIMS1 was significantly upregulated in bladder cancer and circRIMS1 expression was associated with the pathological stage and histological grade of bladder cancer. Inhibition of circRIMS1 suppressed the proliferation, migration and invasion of bladder cancer cells in vitro and in vivo, while overexpression of circRIMS1 exerted the opposite effects. Moreover, the circRIMS1/miR-433-3p/CCAR1 regulatory axis was confirmed to be responsible for the biological functions of circRIMS1. Conclusions: CircRIMS1 acts as a tumor promoter in bladder cancer to enhance tumor growth, migration and invasion via the miR-433-3p/CCAR1 regulatory axis, which provides a new therapeutic target and a novel biomarker in bladder cancer. Keywords: CircRIMS1, Bladder cancer, miR-433-3p, CCAR1, Progression, Metastasis
2020-05-09 | GSE150142 | GEO
Project description:Circular RNAs (circRNAs), a diverse class of ncRNAs highly enriched in developing neurons, play roles in local protein synthesis and synaptic plasticity. However, distinguishing functional from non-functional circRNAs is challenged by their abundance, tissue specificity and splicing variability. To address this, we conducted a RNAi knockdown screen targeting 32 highly expressed, conserved circRNAs enriched in dendritic processes. circRERE isoforms emerged as regulators of dendritic synapse density and electrophysiological characteristics. mRNA-seq supports the dysregulation of synaptic genes, particularly miR-128-3p-sensitive transcripts. MiR-128-3p activity and expression are reduced, with circRERE possessing multiple miR-128-3p binding sites, suggesting a protective interaction supported by a rescue of the synaptic phenotype upon miR-128-3p overexpression. Conversely, circRERE overexpression with intact miR-128-3p sites rescued the synaptic phenotype and independently increased miR-128-3p levels. These findings demonstrate the necessity for the broad characterization of circRNAs in the nervous system to comprehensively understand their influence on essential non-coding RNA regulatory networks.
2024-03-18 | GSE261609 | GEO
Project description:Circular RNAs (circRNAs), a diverse class of ncRNAs highly enriched in developing neurons, play roles in local protein synthesis and synaptic plasticity. However, distinguishing functional from non-functional circRNAs is challenged by their abundance, tissue specificity and splicing variability. To address this, we conducted a RNAi knockdown screen targeting 32 highly expressed, conserved circRNAs enriched in dendritic processes. circRERE isoforms emerged as regulators of dendritic synapse density and electrophysiological characteristics. mRNA-seq supports the dysregulation of synaptic genes, particularly miR-128-3p-sensitive transcripts. MiR-128-3p activity and expression are reduced, with circRERE possessing multiple miR-128-3p binding sites, suggesting a protective interaction supported by a rescue of the synaptic phenotype upon miR-128-3p overexpression. Conversely, circRERE overexpression with intact miR-128-3p sites rescued the synaptic phenotype and independently increased miR-128-3p levels. These findings demonstrate the necessity for the broad characterization of circRNAs in the nervous system to comprehensively understand their influence on essential non-coding RNA regulatory networks.
2024-03-18 | GSE261607 | GEO
Project description:Purpose: To explore the possible pathogenesis of venous thromboembolism from the perspective of circRNAs. Methods: The thrombus model of inferior vena cava in SD rats was established by stenosis method. Peripheral blood samples of DVT rats were collected at 1h, 6h,12h and 3d, which were sequenced with Illumina circRNAs and mRNA. The differential circRNAs and mRNA were analyzed by STEM analysis software. Clusters that can reflect the evolution of thrombus were selected for in-depth analysis, and circRNAs and mRNA were screened according to the pathway enrichment analysis of the selected clusters. Real time fluorescent quantitative PCR (qPCR) was used to verify and determine the candidate circRNAs and mRNA. The function of target circRNA was verified in DVT rats. The interacting miRNAs of circRNAs and mRNA were predicted by online database respectively. Candidate miRNAs were identified by integrating the related information of miRNAs and verified by qPCR. Results:The SD rat model of deep venous thrombosis was successfully established by the stenosis method. In model group, there were 736, 3691, 3406 and 2639 circRNAs up-regulated and 944, 327, 318 and 397 circRNAs down-regulated at 1h, 6h, 12h and 3d, respectively. Compared with Sham group, 169, 885, 298 and 500 mRNA were up-regulated and 231, 291,75 and 73 mRNA were down-regulated at 1h, 6h, 12h and 3d in model group, respectively. STEM analysis found that cluster 45 was similar to thrombus development. The pathway related to platelet function was selected in cluster 45, and 10 circrRNAs and 4 interacting mRNAs were selected for qPCR verification by combining the gene in platelet pathway and annotation gene of cluster 45 and mRNA-circRNA interaction network. According to qPCR results and whether ID is found in rat circRNA database (CIRCpedia-V2), CBT15_circR_3235 (ID in circpedia-v2: rno_CIRCpedia_1953) is determined as the target circRNA. In vivo，knockdown of rno_CIRCpedia_1953 attenuates the formation of DVT in rats. The potential target miRNAs of rno_CIRCpedia_1953 and Tuba4a were predicted by using online miRDB and miRWalk databases respectively, and rno-miR-3543, rno-miR-320-5p and rno-miR-26b-3p are preliminarily identified as potential target miRNAs that rno_CIRCpedia_1953 may combine to play the ceRNA mechanism. Conclusions: Animal model of DVT in rats was successfully established by stenosis method. High-throughput sequencing analysis of circRNAs showed that circRNAs participated in the evolution of DVT. According to STEM functional analysis of mRNA sequencing, a target circRNA rno_CIRCpedia _1953 was screened, verified and identified. rno_CIRCpedia_1953 may participate in the development of DVT by acting as miRNA molecular sponge.
2023-04-01 | GSE148332 | GEO
Project description:The recent reports of two circular RNAs (circRNAs) with strong potential to act as microRNA (miRNA) sponges suggest that circRNAs might play important roles in regulating gene expression. However, the global properties of circRNAs are not well understood. We developed a computational pipeline to identify circRNAs and quantify their relative abundance from RNA-seq data. Applying this pipeline to a large set of non-poly(A)-selected RNA-seq data from the ENCODE project, we annotated 7,112 human circRNAs that were estimated to comprise at least 10% of the transcripts accumulating from their loci. Most circRNAs are expressed in only a few cell types and at low abundance, but they are no more cell-type–specific than are mRNAs with similar overall expression levels. Although most circRNAs overlap protein-coding sequences, ribosome profiling provides no evidence for their translation. We also annotated 635 mouse circRNAs, and although 20% of them are orthologous to human circRNAs, the sequence conservation of these circRNA orthologs is no higher than that of their flanking linear exons. The previously proposed miR-7 sponge, CDR1as, is one of only two circRNAs with more miRNA sites than expected by chance, with the next best miRNA-sponge candidate deriving from a primate-specific zinc-finger gene, ZNF91. These results provide a new framework for future investigation of this intriguing topological isoform while raising doubts regarding a biological function of most circRNAs. Examination of 9 samples in 1 cell type Note: The ENCODE data we used are under GEO SuperSeries GSE26284 (all samples labeled "_cell_total"). But they were not used in the processing of the U2OS data.
2014-07-08 | E-GEOD-51584 | biostudies-arrayexpress
Project description:Circular RNAs (circRNAs) are widespread circular forms of non-coding RNAs with largely unknown function. Because stimulation of mammary cells with the epidermal growth factor (EGF) leads to dynamic changes in the abundance of both coding and non-coding RNA molecules, and culminates in the acquisition of a robust migratory phenotype, this cellular model might disclose functions of circRNAs. Here we show that circRNAs of EGF-stimulated mammary cells are stably expressed, while mRNAs and micro-RNAs change within minutes. In general, the circRNAs we detected are relatively long-lived and weakly expressed. Interestingly, they are almost ubiquitously co-expressed with the corresponding linear transcripts, and the respective, shared promoter regions are more active compared to genes producing linear isoforms only. These findings imply that altered abundance of circRNAs, unlike changes in the levels of other RNAs, might not play critical roles in signaling cascades and downstream transcriptional networks that rapidly commit cells to specific outcomes. Detection of circRNAs from RNA-Seq â triplicate
2015-12-17 | E-GEOD-71195 | biostudies-arrayexpress
Project description:The study aimed to identify circular RNAs (circRNAs) commonly back-spliced to intronic region of different sets of endothelial cells (human cardiac microvascular endothelial cells (HCMEC), human aortic endothelial cells (HAoEC), human umbilical vein endothelial cells (HUVECs)) and to evaluate their overall expression and their expression compared to their respective host gene. Identified circRNAs were quality controlled by their detection in an additional exonuclease RNase R treated RNA-Seq dataset performed with RNA of HUVECs. CircRNAs were compared for overlapping detection between datasets and filtered by annotation for circRNAs back-spliced to intronic regions. Common endothelial intronic circRNAs candidates were compared to respective murine circRNAs stored in the circATLAS database. The prime candidate cZNF292 was functionally characterized in vivo and in vitro.
2023-11-30 | E-MTAB-11171 | biostudies-arrayexpress