Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines

Abstract

Neuroblastoma cell lines are an important and cost-effective model used to study oncogenic drivers of the disease. While many of these cell lines have been previously characterized with SNP, methylation, and/or mRNA expression microarrays, there has not been an effort to comprehensively sequence these cell lines. Here, we present raw whole transcriptome data generated by RNA sequencing of 39 commonly-used neuroblastoma cell lines. These data can be used to perform differential expression analysis based on a genetic aberration or phenotype in neuroblastoma (e.g., MYCN amplification status, ALK mutation status, chromosome arm 1p, 11q and/or 17q status, sensitivity to pharmacologic perturbation). Additionally, we designed this experiment to enable structural variant and/or long-noncoding RNA analysis across these cell lines. Finally, as more DNase/ATAC and histone/transcription factor ChIP sequencing is performed in these cell lines, our RNA-Seq data will be an important complement to inform transcriptional targets as well as regulatory (enhancer or repressor) elements in neuroblastoma.

Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma

“…Similar to other members of the glypican family, GPC2 is expressed on neuroblastoma cells as both a core 62 kDa protein, and also as a higher molecular weight glycanated GPC2 species (80-100 kDa) with glycosaminoglycan post-translation modifications (Figures 3A-C and S3A; Table S1). GPC2 expression quantified by Western blot across our neuroblastoma cell panel (Figure 3C; Table S1) correlated strongly with GPC2 expression measured by RNA sequencing (Pearson r = 0.57, p < 0.01) (Harenza et al, 2017). We additionally performed immunohistochemistry (IHC) on eight of these neuroblastoma cell lines, showing dense GPC2 staining in a membranous pattern and in exact accordance with our Western blotting data (Figures 3C, 3D, and S3B; Table S1).…”

“…Neuroblastoma cell lines were profiled by RNA and targeted DNA sequencing as previously described (Harenza et al, 2017; Hart et al, 2017) and neuroblastoma cell line GPC2 FPKM, MYCN amplification status, and TP53 and ALK mutation status was queried from these data sets.…”

Glio‐ and neuro‐protection by prosaposin is mediated by orphan G‐protein coupled receptors GPR37L1 and GPR37

“…The first cells used to demonstrate a protective potential of PSAP were mouse neuroblastoma NS20Y and human neuroblastoma SK-N-MC cells (O'Brien et al, 1994). Interestingly, the neuroblastoma lines closely related to SK-N-MC express substantial levels of GPR37 (Harenza et al, 2017). Published transcriptomes of astrocytes (Anderson et al, 2016;Chai et al, 2017;Zhang et al, 2014;Zhang et al, 2016) and our own data (Supporting Information Figures S2 and S3) unequivocally demonstrate that astrocytes of various parts of the central nervous system express high levels of GPR37L1 while the level of GPR37 is generally much lower.…”

Investigating piwi‐interacting RNA regulome in human neuroblastoma

“…In this current approach, we obtained the set of 3940 differentially expressed genes (DE) from the transcriptomic profiling of 39 commonly-used NB cell lines performed by Harenza et al 31 In this current approach, we obtained the set of 3940 differentially expressed genes (DE) from the transcriptomic profiling of 39 commonly-used NB cell lines performed by Harenza et al 31 …”

“…).We obtained these sets of repeat-containing transcripts by parsing 3940 differentially expressed genes in 39 NB cells reported by Harenza et al31 through RepeatMasker 32. ).We obtained these sets of repeat-containing transcripts by parsing 3940 differentially expressed genes in 39 NB cells reported by Harenza et al31 through RepeatMasker 32.…”