Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hsa_circRNA_G004213 Promotes Cisplatin Sensitivity by Regulating miR-513b-5p/PRPF39 in Liver Cancer

ABSTRACT: Purpose:In recent years, increasing evidence has confirmed that exosomal circular RNAs (circRNAs) play a crucial role in the prognostic prediction and diagnosis of liver cancer （LC）. In this study, we first compared the expression patterns of exosomal circRNAs during transarterial chemoembolization (TACE). Methods:CircRNA-seq identified 390 differentially expressed circRNAs between the prior TACE and TACE1 groups and 489 differentially expressed circRNAs between the prior TACE and TACE2 groups. GO analysis of the differentially expressed circRNAs showed that they were associated with fatty acid metabolism, receptor binding and membrane protein complexes. KEGG pathway analysis predicted that protein digestion and absorption pathways were activated after TACE. And we screened out a novel gene , hsa_circRNA_G004213 (circ_G004213) was significantly upregulated after TACE (fold change >10, P<0.01). Further analysis found circ_G004213 significantly increased the cisplatin sensitivity of HepG2 cells and positively correlated with the prognosis of tumor-bearing mice. Based on the potential downstream miRNAs and mRNAs, the circRNA‐miRNA-mRNA network was constructed. Results: We demonstrated that circ_G004213 regulates cisplatin resistance via the miR-513b-5p/PRPF39 axis. Finally, our study confirmed that circ_G004213 was positively correlated with the prognosis of LC patients after TACE. Therefore, circ_G004213 may be used as an indicator for predicting the efficacy of TACE. Conclusions: Hsa_circRNA_G004213 Promotes Cisplatin Sensitivity by Regulating miR-513b-5p/PRPF39 in Liver Cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE165183 | GEO | 2021/01/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

circRNA, lncRNA and mRNA profiles of umbilical cord blood exosomes from preterm newborns showing bronchopulmonary

Project description:Purpose: The purpose of this study was to detect the expression profiles of circRNAs, lncRNAs and mRNAs in umbilical cord blood (UCB) exosomes from BPD infants. Methods:Microarray analysis was performed to compare the RNA profiles of UCB-derived exosomes from preterm newborn with and without BPD. Then, circRNA/lncRNA-miRNA-mRNA co-expression networks were built to determine their associations with BPD.Results:A total of 317 circRNAs, 104 lncRNAs, 135 mRNAs showed significant differential expression in UCB-derived exosomes from BPD preterm infants compared with the NBPD group. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted for examining differentially expressed exosomal circRNAs, lncRNAs and mRNAs. Our results showed the GO terms and KEGG pathways mostly involving differentially expressed exosomal RNAs were closely associated with endothelial or epithelial cell development. In addition, two networks were identified, including circRNA-circ_0086018/miR-762/MEN1 and lncRNA-BASP1-AS1/miR-20a-5p/DNAJC22 networks, which may take part in BPD.

2022-08-31 | GSE190215 | GEO

Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed

Project description:Circular RNAs (circRNAs) are an endogenous class of animal RNAs. Despite their abundance, their function and expression in the nervous system are unknown. Therefore, we sequenced RNA from different brain regions, primary neurons, isolated synapses, as well as during neuronal differentiation. Using these and other available data, we discovered and analyzed thousands of neuronal human and mouse circRNAs. circRNAs were extraordinarily enriched in the mammalian brain, well conserved in sequence, often expressed as circRNAs in both human and mouse, and sometimes even detected in Drosophila brains. circRNAs were overall upregulated during neuronal differentiation, highly enriched in synapses, and often differentially expressed compared to their mRNA isoforms. circRNA expression correlated negatively with expression of the RNA-editing enzyme ADAR1. Knockdown of ADAR1 induced elevated circRNA expression. Together, we provide a circRNA brain expression atlas and evidence for important circRNA functions and values as biomarkers. To assess circRNA expression in mammalian brain, we sequenced and analyzed mouse brain regions (hippocampus, cerebellum, prefrontal cortex and olfactory bulb), various neuronal differentiation (mouse P19 and human SH-SY5Y cells) and maturation (mouse cortical neurons) stages, and subcellular compartments in mouse (synaptoneurosomal fraction, cytoplasmic fraction, whole brain lysate).

2015-04-24 | E-GEOD-65926 | biostudies-arrayexpress

High-throughput Sequencing of exosomal circRNAs in large artery atherosclerotic stroke

Project description:Exosomal circRNA sequencing was used to identify differentially expressed circRNAs between LAA stroke and normal controls. From a further validation stage, the results were validated using RT-qPCR.

2022-02-02 | GSE190869 | GEO

rat bladder LC-MS/MS proteomics

Project description:Objective: Bladder outlet obstruction (BOO) is a common urologic disease associated with poorly understood molecular mechanisms. This study aimed to investigate the possible involvements of circRNAs (circular RNAs) and circRNA-encoded proteins in BOO development. Methods: The rat BOO model was established by the partial bladder outlet obstruction surgery. Differential expression of circRNA and protein profiles were characterized by deep RNA sequencing and iTRAQ quantitative proteomics respectively. Novel proteins encoded by circRNAs were predicted through ORF (open reading frame) selection using the GETORF software and verified by the mass spectrometry in proteomics, combined with the validation of their expressional alterations by quantitative RT-PCR. Results: Totally 3051 circRNAs were differentially expressed in bladder tissues of rat BOO model with widespread genomic distributions, including 1414 up-regulated and 1637 down-regulated circRNAs. Our following quantitative proteomics revealed significant changes of 85 proteins in rat BOO model, which were enriched in multiple biological processes and signaling pathways such as the PPAR and Wnt pathways. Among them, 21 differentially expressed proteins were predicted to be encoded by circRNAs and showed consistent circRNA and protein levels in rat BOO model. The expression of five protein-encoding circRNA were further validated by quantitative RT-PCR and mass spectrometry. Conclusion: The circRNA and protein profiles were substantially altered in rat BOO model, with great expressional changes of circRNA-encoded novel proteins.

2022-02-22 | PXD029337 | Pride

Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals

Project description:Circular RNAs (circRNAs) are a large class of animal RNAs. To investigate possible circRNA functions, it is important to understand circRNA biogenesis. Besides human Alu repeats, sequence features that promote exon circularization are largely unknown. We experimentally identified new circRNAs in C. elegans. Reverse complementary sequences between introns bracketing circRNAs were significantly enriched compared to linear controls. By scoring the presence of reverse complementary sequences in human introns we predicted and experimentally validated novel circRNAs. We show that introns bracketing circRNAs are highly enriched in RNA editing or hyper-editing events. Knockdown of the double-strand RNA editing ADAR1 enzyme significantly and specifically up-regulated circRNA expression. Together, our data support a model of animal circRNA biogenesis in which competing RNA:RNA interactions of introns form larger structures which promote circularization of embedded exons, while ADAR1 antagonizes circRNA expression by melting stems within these interactions. Thus, we assign a new function to ADAR1. Examination of 12 samples in different stages of C.elegans development.

2015-01-06 | E-GEOD-63823 | biostudies-arrayexpress

RNA-Seq profiling of circular RNAs in colorectal cancer and circST7L as a potential biomarker

Project description:Aberrant expression of circular RNAs (circRNAs) has been reported in a variety of cancers. CircRNAs may serve as candidate biomarkers and have implications for cancer diagnosis and treatment. RNA-sequencing (RNA-seq) was applied to detect circRNA expression in five CRC and paired normal tissues. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was performed to measure circRNA expression, and the receiver operating characteristic curve was used to assess the diagnostic value of circRNA as a biomarker in 50 patients. A total of 1602 circRNAs were differentially expressed, including 743 upregulated and 859 downregulated circRNAs in CRC. CircST7L (hsa_circ_0110464) has a high diagnostic value for CRC. The expression of circST7L was closely associated with tumor size (P=0.024), grade (P=0.017), depth of invasion (P=0.034) and lymph node metastasis (P=0.001). In addition, prediction of circRNA-miRNA interactions identified miR-6821-5p, miR-1908-3p, and miR-6748-5p as pivotal targets of differentially expressed circRNAs. Finally, we predicted 7 miRNAs that may bind to circST7L and 13 target genes for these miRNAs. This study demonstrated that circRNAs were differentially expressed between CRC and normal tissues, and suggested that circST7L might be a promising diagnostic biomarker for CRC.

2023-09-01 | GSE235850 | GEO

Development of circRNAs expression signatures in exosomes derived from different gastric cancer cells

Project description:Exosomes from the culture media (CM) of four GC cells (GCCs) and human gastric epithelial cells were isolated. Exosomal RNA was extracted, and circRNA microarray assay was performed to identify GC-specific exosomal circRNAs. A total of 58 exosomal circRNAs were expressed at considerable higher levels in GCCs than those in normal controls.The expression level of several top upregulated circRNAs were detected using qRT-PCR in both GC cells and clinical specimens of GC patients. More interesting, besides the high expression in GC cell derived exosomes, hsa_circ_0015286 was the uniquely upregulated circRNA in the plasma exosomes and tissues of GC patients..The result suggested that exosomal hsa_circ_0015286 may be a potential noninvasive biomarker for the diagnosis and prognosis monitoring of GC.

2022-05-12 | GSE202538 | GEO

CircRNA_051778 in Exosomes as A Potential Biomarker for Distinguishing Lung Adenocarcinoma-Associated Malignant Pleural Effusion from Tuberculous Pleural Effusion

Project description:We profiled the exosomal circRNA in lung adenocarcinoma-associated malignant (LA-MPE) and tuberculous (TPE) pleural effusion samples by circRNA microarray to determine the potential functions and diagnostic value of the differential expressed circRNAs (DECs)

2022-04-01 | GSE171540 | GEO

Structured elements drive circular RNA translation and expand the human proteome, part4

Project description:The human genome encodes tens of thousands circular RNAs (circRNAs) whose levels correlate with many disease states. While studies have focused on the non-coding functions of circRNAs, emerging evidence suggests that a handful of circRNAs encode proteins. Translation canonically starts by recognition of mRNA 5’cap and scanning to the start codon; how circRNA translation initiates remains unclear. Here, we developed a high-throughput screen to systematically identify and quantify RNA sequences that can direct circRNA translation. We identify and validate over 17,000 circRNA internal ribosome entry sites (IRES) and reveal that 18S rRNA complementarity and a structured RNA element on the IRES are important for facilitating circRNA cap-independent translation. With genomic and peptidomic analyses of the IRES, we identified nearly 1,000 putative endogenous protein-coding circRNAs and hundreds of translational units encoded by these circRNAs. We further characterized circFGFR1p, a protein encoded by circFGFR1, functions as a negative regulator of FGFR1 to suppress cell growth under stress conditions. The circRNA proteome may be important links among circRNA, biological control, and disease.

2021-08-26 | PXD025203 | Pride

Structured elements drive circular RNA translation and expand the human proteome, part1

2021-08-23 | PXD024993 | Pride