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Transcriptomic analysis of gastric cancer cells in response to stable over-expression of circRNA derived from hnRNPU (circ-hnRNPU)

ABSTRACT: Transcriptomic analysis of gastric cancer cells in response to stable over-expression of circRNA derived from hnRNPU (circ-hnRNPU)

PROVIDER: PRJNA1034984 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26639126_1.fastq.gz	Fastqsanger.gz
	SRR26639126_2.fastq.gz	Fastqsanger.gz
	SRR26639127_1.fastq.gz	Fastqsanger.gz
	SRR26639127_2.fastq.gz	Fastqsanger.gz
	SRR26639128_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Transcriptomic analysis of gastric cancer cells in response to stable over-expression of circRNA derived from hnRNPU (circ-hnRNPU)

Project description:Circular RNA (circRNA) is a type of endogenous single-stranded and covalently closed non-coding RNA that plays emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of circRNAs in regulating gastric cancer progression still remain elusive. We identify circ-hnRNPU, a circRNA derived from exons 5, 6, 7 and 8 of heterogeneous nuclear ribonucleoprotein U (hnRNPU), as a tumor suppressor of gastric cancer progression. To investigate the mechanisms underlying the functions of circ-hnRNPU, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human gastric cancer MKN-45 and AGS cells in response to stable over-expression of circ-hnRNPU. The results showed that stable over-expression of circ-hnRNPU led to altered expression of 112 human mRNAs, including 64 up-regulated and 48 down-regulated genes, in both MKN-45 and AGS cells. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to circ-hnRNPU over-expression in human gastric cancer cells, and these findings will help us understand the pathogenesis of cancer progression.

2024-11-02 | GSE246847 | GEO

Transcriptomic analysis of gastric cancer cells in response to stable over-expression of circular RNA derived from CTNNB1 gene (circ-CTNNB1)

Project description:Circular RNAs (circRNAs), a subclass of noncoding RNAs characterized by covalently closed continuous loops, play emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of circRNAs in regulating the Wnt/β-catenin signaling and cancer progression still remain elusive. We identify one intronic circRNA derived from CTNNB1 (circ-CTNNB1) as a novel driver of cancer progression. To investigate the mechanisms underlying the oncogenic functions of circ-CTNNB1, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human gastric cancer AGS cells in response to stable over-expression of circ-CTNNB1. The results showed that stable over-expression of circ-CTNNB1 led to altered expression of 2230 human mRNAs, including 1244 up-regulated genes and 986 down-regulated genes. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to circ-CTNNB1 over-expression in human cancer cells, and these findings will help us understand the pathogenesis of cancer progression.

2019-09-30 | GSE120496 | GEO

Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of circular RNA derived from CUX1 gene (circ-CUX1)

Project description:Circular RNAs (circRNAs), a subclass of noncoding RNAs characterized by covalently closed continuous loops, play emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of circRNAs in regulating neuroblastoma progression still remain elusive. We identify one circRNA derived from CUX1 (circ-CUX1) as a novel driver of neuroblastoma progression. To investigate the mechanisms underlying the oncogenic functions of circ-CUX1, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human neuroblastoma IMR32 cells in response to stable over-expression of circ-CUX1. The results showed that stable over-expression of circ-CUX1 led to altered expression of 1215 human mRNAs, including 781 up-regulated genes and 434 down-regulated genes. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to circ-CUX1 over-expression in human tumor cells, and these findings will help us understand the pathogenesis of tumor progression.

2019-11-07 | GSE136135 | GEO

circ-ZNF609 regulates G1-S progression in Rhabdomyosarcoma

Project description:Circular RNAs (circRNAs) represent a class of covalently closed RNAs, derived from a non-canonical splicing event, ubiquitously expressed among Eukaryotes and conserved among different species. We identified a circRNA (circ-ZNF609) involved in the regulation of human primary myoblast proliferation. Upon its depletion, the percentage of proliferating myoblasts was highly reduced. To deepen our knowledge about circ-ZNF609 role in cell cycle regulation, we studied its expression and function in Rhabdomyosarcoma (RMS), a pediatric skeletal muscle malignancy. We found that circ-ZNF609 is up-regulated in biopsies from both the two major RMS subtypes, the alveolar (ARMS) and the embryonal (ERMS), and we discovered that its knock-down blocks proliferation of an ERMS-derived cell line, while it has no effect on ARMS-derived cells. To understand the mechanism through which circ-ZNF609 affects cell proliferation we compared the different effects of circ-ZNF609 depletion in ERMS and ARMS and we identified genes and pathways on which the circRNA acts.

2018-12-14 | GSE117609 | GEO

A peptide CORO1C-47aa encoded by circ-0000437 functions as a negative regulator in endometrium tumor angiogenesis

Project description:Circular RNAs (circRNA) are a novel class of widespread non-coding RNAs (ncRNAs) that regulate gene expression in mammals. Recent studies demonstrate that functional peptides can be encoded by short open reading frames (sORFs) in ncRNAs, including circRNAs. In this study, through deep RNA sequencing on human endometrial cancer (EC) samples and their paired adjacent normal tissues, we uncovered that the circRNA hsa-circ-0000437 is significantly reduced in EC compared to matched paracancerous tissue. The hsa-circ-0000437 contains a sORF encoding a functional peptide termed as CORO1C-47aa. Overexpression of CORO1C-47aa is capable of inhibiting angiogenesis at the initiation stage by suppressing endothelial cell proliferation, migration, and differentiation through competing with TACC3 to bind to ARNT and suppress VEGF. The anti-tumor effects of CORO1C-47aa on EC progression suggest that CORO1C-47aa has a potential value in anti-carcinoma therapies and deserves further investigation.

2022-02-17 | PXD026046 | Pride

Circ-Phkb promote LPS-induced acute lung injury via the TLR4/MyD88/NF-κB /CCL2 axis

Project description:Our results showed that both circRNA and mRNA profiles are different from those of the sham group. A significant upregulation of circ-Phkb was observed in NR8383 cells and rats exposed to LPS. When circ-Phkb expression was reduced in NR8383 cells, apoptosis and inflammation were greatly reduced, and cell proliferation was increased, while overexpression of circ-Phkb have the opposite effect. In terms of mechanism, circ-Phkb suppression inhibits CCL2 expression via TLR4/MyD88/NF-κB pathway.

2024-02-07 | GSE226036 | GEO

Therapeutic SHPRH-146aa encoded by circ-SHPRH dynamically upregulates P21 to inhibit CDKs in neuroblastoma

Project description:Recent research has underscored the significance of circular RNA (circRNA) in various cancers, including neuroblastoma (NB). Specifically, circ-SHPRH, a distinct circRNA, has emerged as an inhibitor of tumor growth through its ability to sequester miRNAs or produce the SHPRH-146aa protein. To explore circ-SHPRH's involvement in NB and its potential application in gene therapy, this study examined its expression in 94 NB tissues and cell lines (SK-N-BE(2), SH-SY5Y, CHLA-255) using real-time PCR and fluorescence in situ hybridization (FISH). Functional assays encompassing both overexpression and knockdown experiments in NB cell lines, as well as in vivo investigations, were conducted. RNA-seq analysis revealed a correlation between circ-SHPRH and the P21 (CDKN1A) pathway, a pivotal cell cycle regulator. Validation through PCR and other techniques confirmed that circ-SHPRH upregulated P21 expression. Furthermore, the regulatory role of circ-SHPRH in the P21-CDK pathway was corroborated through SHPRH-146aa expression. Notably, adenovirus-mediated overexpression of circ-SHPRH effectively curbed NB tumor growth in NSG mice, while combining circ-SHPRH with everolimus exhibited potential for NB treatment. This study elucidates the remarkable significance of circ-SHPRH in NB and its prospective utility in gene therapy, thereby paving the way for innovative therapeutic approaches.

2024-07-19 | GSE244294 | GEO

The mechanism of circ-ARAP2 regulation of tumor EMT and stem cell differentiation affecting proliferation, invasion and chemotherapy resistance of Esophageal Squamous Cell Carcinoma

Project description:Circular RNAs (circRNAs) belong to a novel class of noncoding RNA that gained more attention in human cancer pathogenesis. The circRNA roles in esophageal squamous cell carcinoma (ESCC) is unknown. Present investigation was to characterize new circRNAs regulating ESCC progression and explore the regulatory mechanisms in ESCC. In this study, circRNAs differentially expressed in ESCC and adjacent normal tissues were characterized via high-throughput sequencing. We then investigated the effects of the differentially expressed circRNA ARFGAP with RhoGAP domain, ankyrin repeat and PH domain 2 (circ-ARAP2) on tumor progression in vivo and in vitro. We used luciferase reporter assays to identify the relationships between circ-ARAP2, its target microRNA (miR)-761 and the cell cycle regulator Forkhead Box M1 (FOXM1). Expression profile analyses regarding human circRNAs in ESCC demonstrated that circ-ARAP2 was up-regulated significantly in ESCC tissues and cell lines. The circ-ARAP2 down-regulation suppressed ESCC proliferation, tumor growth and metastasis in vivo and in vitro. The data also suggested that miR-761 and FOXM1 were circ-ARAP2 downstream targets which were confirmed through luciferase reporter analysis. Overexpression of FOXM1 or inhibiting miR-761 slowed ESCC cell proliferation and invasion after silencing circ-ARAP2. circ-ARAP2 also influenced the endothelial-mesenchymal transition (EMT) and cancer stem cells differently by regulating miR-761/FOXM1. In one word, the results demonstrated that abnormal circ-ARAP2 expression promoted ESCC progression by regulating miR-761/FOXM1 axis-mediated stemness and EMT.

2024-07-03 | GSE179757 | GEO

Transcriptomic analysis of gastric cancer cells in response to stable over-expression of circular RNA derived from CTNNB1 gene (circ-CTNNB1)

Project description:Transcriptomic analysis of gastric cancer cells in response to stable over-expression of circular RNA derived from CTNNB1 gene (circ-CTNNB1)

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HNRNPU regulates lncRNAs nuclear localization

Project description:To elucidate the role of HNRNPU in regulation of lncRNAs nuclear localization, we knocked down HNRNPU in K562 cells using short interfering RNAs and performed subcellular RNA-seq using nuclear or cytosolic RNAs

2021-01-23 | GSE165310 | GEO

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