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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: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE136135 | GEO | 2019/11/07

REPOSITORIES: GEO

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

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

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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.

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2018-12-14 | GSE117609 | GEO

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