GSE171379
Gene expression profiles of BrdU-treated BE(2)N during conversion from adrenergic to mesenchymal cell lineages
Purpose: Treatment of neuroblastoma cell liner BE(2)N is known to convert these cells from adrenergic morphology to one that resembles mesenchymal cells. The goal of this study is to characterize the transcriptomes of BE(2)N during the conversion process and determine if the transcription changes are consistent with previously defined ADRN and MES signature genes. Methods: BE2N cells were treated with DMSO for 26 days or with 10µM BrdU for 5, 11, 20 and 26 days. Total RNA was isolated with the RNeasy Mini kit (Qiagen), and the quality of the preparations assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies).  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), 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). The fold changes were calculated by directly comparing the FPKM values of samples and controls. Results: The gene expression changes in BrdU-treated BE2N cells were identified through comparison with DMSO-treated control cells. 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 BrdU triggers the transcriptional re-programming of ADRN cells into MES cells. Conclusion: This study indicates that the morphologic conversion mediated by BrdU treatment of neuroblastoma cells is accompanied by genome wide transcriptional re-programming. Overall design: mRNA profiles of BE(2)N cells treated with DMSO for 26 days and with 10 µM BrdU for 5, 11, 20, and 26 days