Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of cellular nucleic acid binding protein (CNBP)

Cellular nucleic acid binding protein (CNBP) is a 19 kDa conserved protein containing seven tandem cysteine-cysteine-histidine-cysteine zinc finger repeats. However, the action modes and underlying mechanisms of CNBP in NB progression remain largely unknown. We identify CNBP as an independent prognostic factor for poor outcome of neuroblastoma. CNBP exerts oncogenic roles in ribosome biogenesis, tumorigenesis, and aggressiveness. To investigate the mechanisms underlying the oncogenic functions of CNBP, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human neuroblastoma IMR-32 cells in response to stable over-expression of CNBP. The results showed that stable over-expression of CNBP led to altered expression of 3524 human mRNAs, including 889 up-regulated genes and 2635 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 CNBP over-expression in human tumor cells, and these findings will help us understand the pathogenesis of tumor progression. Total RNA of cells stably transfected with empty vector or CNBP was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an Illumina HiSeq X Ten platform were performed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.