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Epigenomic profiling of neuroblastoma cell lines

ABSTRACT: Understanding the aberrant transcriptional landscape of neuroblastoma is necessary to provide insight to the underlying influences of the initiation, progression and persistence of this developmental cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic transcription factors, MYCN and MYC, as well as regulatory histone marks H3K4me1, H3K4me3, H3K27Ac, and H3K27me3 in ten commonly used human neuroblastoma-derived cell line models. In addition, for all of the profiled cell lines we provide ATAC-Seq as a measure of open chromatin. We validate specificity of global MYCN occupancy in MYCN amplified cell lines and functional redundancy of MYC occupancy in MYCN non-amplified cell lines. Finally, we show with H3K27Ac ChIP-Seq that these cell lines retain expression of key neuroblastoma super-enhancers (SE). We anticipate this dataset, coupled with available transcriptomic profiling on the same cell lines, will enable the discovery of novel gene regulatory mechanisms in neuroblastoma. This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE138315 | GEO | 2019/11/03

REPOSITORIES: GEO

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Project description:In neuroblastoma, amplification of the oncogenic basic helix-loop-helix (bHLH) transcription factor (TF) MYCN is the defining prognosticator of high-risk disease, occurs in one-third of neuroblastoma, and drastically reduces overall survival rates. As a proto-oncogene, targeted MYCN overexpression in peripheral neural crest is sufficient to initiate disease in mouse models. In MYCN amplified neuroblastoma, elevated expression of the factor is crucial to maintain tumor stemness and is associated with increased proliferation and aberrant cell cycle progression, as these tumors lack the ability to arrest in G1 in response to irradiation. MYCN down-regulation broadly reverses these oncogenic phenotypes in a variety of neuroblastoma models and recent thereapeutic strategies to indirectly target MYCN production or protein stability have reduced tumor growth in vivo. These observations motivate an investigation of MYCN binding in MYCN amplified tumors as it remains fundamentally unclear how elevated levels of the factor occupy the genome and alter transcriptional programs in neuroblastoma. Here we present the first dynamic chromatin and transcriptional landscape of direct MYCN perturbation in neuroblastoma. We find that at oncogenic levels, MYCN associates with E-box (CANNTG) binding motifs in an affinity dependent manner across most active cis-regulatory promoters and enhancers. MYCN shutdown globally reduces histone acetylation and transcription, consistent with prior descriptions of MYC proteins as non-linear amplifiers of gene expression. We establish that MYCN load at the promoter and proximal enhancers predicts transcriptional responsiveness to MYCN shutdown and that MYCN enhancer binding occurs prominently at the most strongly occupied and down-regulated genes, suggesting a role for these tissue specific elements in predicating MYCN responsive âtargetâ genes. At these invaded enhancers, we identify the lineage specific bHLH TWIST1 as a key collaborator and dependency of oncogenic MYCN. These data suggest that MYCN enhancer invasion helps shape transcriptional amplification of the neuroblastoma gene expression program to promote tumorigenesis. ChIP-Seq in SHEP21, BE2C, KELLY, and NGP neuroblastoma cell lines for H3K27ac, H3K4me3, RNA PolII, MYCN, BRD4, or TWIST1

Project description:MYCN is an oncogene amplified in approximately 20% of all neuroblastomas and 50% of high risk neuroblastoma. It is a transcription factor regulating the expression of genes involved in proliferation and apoptosis.We would like to identify genes potentially regulated by MYCN in a conditional MYCN expression system. The SHEP Tet21N system is a conditional, tetracycline-regulated MYCN expression system established in the MYCN non-amplified SHEP neuroblastoma cell line (Lutz et al., 1996). Expression of MYCN is switched off by the addition of tetracycline to the growth medium. Levels of MYCN protein and RNA in the absence of tetracycline are comparable with those present in MYCN amplified cell lines (Bell et al., 2006). By performing microarray analyses on the Tet21n cell lines in the presence and absence of MYCN we hope to identify genes whose expression had been altered by MYCN either upregulated or downregulated and may be potential MYCN targets. The altered expression of some of these genes will then be validated using quantitative RTPCR and a selection will be further investigated to determine if they are MYCN transcriptional targets and may be potential candidates for anti-MYCN therapies for neuroblastoma Specific objectives 1) To investigate genes which are altered by 2 fold or more in the presence of or absence of MYCN in Tet21N cells. Refs: Bell, E., Premkumar, R., Carr, J., Lu, X., Lovat, P.E., Kees, U.R., Lunec, J. & Tweddle, D.A. (2006). The role of MYCN in the failure of MYCN amplified neuroblastoma cell lines to G1 arrest after DNA damage. Cell Cycle, 5, 2639-47. Lutz, W., Stohr, M., Schurmann, J., Wenzel, A., Lohr, A. & Schwab, M. (1996). Conditional expression of N-myc in human neuroblastoma cells increases expression of alpha-prothymosin and ornithine decarboxylase and accelerates progression into S-phase early after mitogenic stimulation of quiescent cells. Oncogene, 13, 803-12.

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Epigenomic profiling of neuroblastoma cell lines

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