GSE171380
Gene expression profiles of  BE(2)N expressing Dn-hTERT
Purpose: Infection of neuroblastoma cell liner BE(2)N with a retroviral vector that overexpressed Dn-hTERT caused the conversion of these cells from adrenergic morphology to one that resembles mesenchymal cells. During prolonged passage, down-regulation of Dn-hTERT expression caused a reversal in cell morphology (i.e., from mesenchymal to adrenergic cells). The goal of this study is to characterize the transcriptomes of BE(2)N during the morphologic conversion and reversal and determine if the transcription changes are consistent with previously defined ADRN and MES signature genes. Methods: Total RNA was isolated from parental BE2N cells and cells infected with Dn-hTERT retrovial vector at day 33, day 55, and day 82 post infection. TruSeq stranded mRNA  libraries were prepared and sequenced with paired-end 50 bps on Illumina NovaSeq 6000 by the WCM Genomics Core Facility.  The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.  RNA reads were aligned and mapped to theGRCh37 human reference genome by STAR (Version2.5.2) (https://github.com/alexdobin/STAR) 56, and transcriptome reconstruction was performed by Cufflinks (Version 2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/).  The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM) 57, 58. The fold changes were calculated by directly comparing the FPKM values of samples and controls. Results: The gene expression changes in Dn-hTERT treated cells were identified. The list of up-regulated and down-regulated genes were found to overlap strongly with previously defined MES and ADRN signature genes, supporting the notion that Dn-hTERT triggers the transcriptional re-programming of ADRN cells into MES cells. Conclusions: This study demonstrates that the morphologic conversion mediated by inhibition of telomerase in neuroblastoma cells is accompanied by genome wide transcriptional re-programming. Overall design: mRNA profiles of parental BE(2)N cells and cells infected with Dn-hTERT expressing retrovirus for 33, 55, and 82 days