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

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

PROVIDER: PRJNA561358 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10010277_1.fastq.gz	Fastqsanger.gz
	SRR10010277_2.fastq.gz	Fastqsanger.gz
	SRR10010278_1.fastq.gz	Fastqsanger.gz
	SRR10010278_2.fastq.gz	Fastqsanger.gz

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Similar Datasets

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

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 exons (ecircCUX1)

Project description:Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining of public datasets, we identified circular RNA derived from CUX1 exons (ecircCUX1) as a novel driver of NB progression. To investigate the mechanisms underlying the oncogenic functions of ecircCUX1, we employed the BGIseq500 as a discovery platform to analyze the transcriptome profiling changes of human SH-SY5Y cells in response to stable over-expression of ecircCUX1. The results showed that stable over-expression of ecircCUX1 led to altered expression of 2155 human mRNAs, including 460 up-regulated and 1695 down-regulated genes. Then, we found the possible roles of these differentially regulated mRNAs in selected pathways including lipid metabolic reprogramming, mitochondrial complex I activity, invasion, and metastasis by Bioinformatic analysis. 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 ecircCUX1 over-expression in human NB cells, and these findings will help us understand the pathogenesis of NB.

2021-10-06 | GSE182329 | GEO

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 neuroblastoma cells in response to stable over-expression of circular RNA derived from CUX1 exons (ecircCUX1)

Project description:Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of circular RNA derived from CUX1 exons (ecircCUX1)

| PRJNA755868 | ENA

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

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)

| PRJNA493202 | ENA

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

Transcription profiling : Stable knockdown CUX1 knockdown in LOUCY cells lines

Project description:LOUCY cells were resuspended in Opti-MEM (Gibco) and electroporated in 4 mm cuvettes (300 V, 1000 F; Genepulser XCell, Bio-Rad) using Stealth siRNAs (Ambion) against CUX1 or negative control duplexes. Cells were rested for 15 min following electroporation before dilution into normal RPMI 10 percent FBS growth media. RNA prepared from cells 48-72 h later using an RNeasy mini kit (Qiagen) was used for cDNA preparation for microarrays according to manufacturers instructions (Illumina).

2013-11-05 | E-MTAB-1833 | biostudies-arrayexpress

Genomic studies controvert the existence of the CUX1 p75 isoform

Project description:CUX1, a homeodomain-containing transcription factor, is recurrently deleted or mutated in multiple tumor types. In myeloid neoplasms, CUX1 deletion or mutation carries a poor prognosis. We have previously established that CUX1 functions as a tumor suppressor in hematopoietic cells across multiple organisms. Others, however, have described oncogenic functions of CUX1 in solid tumors, often attributed to truncated CUX1 isoforms, p75 and p110. Given the clinical relevance, it is imperative to clarify these discrepant activities. Herein, we sought to determine the CUX1 isoforms expressed in hematopoietic cells, and find that they express the full-length p200 isoform. Through the course of this analysis, we found no evidence of the p75 alternative transcript in any cell type examined. Using an array of orthogonal approaches, including biochemistry, proteomics, CRISPR/Cas9 genomic editing, and analysis of functional genomics datasets across a spectrum of normal and malignant tissue types, we found no data to support the existence of the CUX1 p75 isoform generated by an alternative transcriptional start site. Based on these results, prior studies of p75 require reevaluation, including the interpretation of oncogenic roles attributed to CUX1.

2022-02-17 | PXD027527 | Pride

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