Transcriptomic analysis of neuroblastoma SH-SY5Y cells in response to stable over-expression of neuroblastoma highly expressed 1 (NHEG1)

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 public microarray and RNA sequencing datasets, we identified neuroblastoma highly expressed 1 (NHEG1) as a novel 1360-bp lncRNA associated with poor outcome of NB. To investigate the mechanisms underlying the oncogenic functions of NHEG1, we employed the human whole genome microarray expression profiling as a discovery platform to analyze the transcriptome profiling changes of human SH-SY5Y cells in response to stable over-expression of NHEG1. The results showed that stable over-expression of NHEG1 led to altered expression of 869 human mRNAs, including 499 up-regulated genes and 370 down-regulated genes. Then we found the possible roles of these differentially regulated mRNAs in selected pathways including cell cycle/proliferation, apoptosis, and cytokine/chemokine responses by Bioinformatic analysis. Furthermore, we validated the microarray results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to NHEG1 over-expression in human NB cells, and these findings will help us understand the pathogenesis of NB. Total RNA of cells stably transfected with empty vector or NHEG1 was extracted using the TRIZOL Reagent according to the manufacturer's instructions. Gene expression profiling was performed for each RNA sample separately on the Affymetrix Human Transcriptome Array 2.0 at Shanghai Technology Corporation (Shanghai, China), in which GeneChip microarray service was certificated by Affymetrix.