Neuroblastoma is composed of two super-enhancer-associated differentiation states

Abstract

Neuroblastoma and other pediatric tumors show a paucity of gene mutations, which has sparked an interest in their epigenetic regulation. Several tumor types include phenotypically divergent cells, resembling cells from different lineage development stages. It has been proposed that super-enhancer-associated transcription factor (TF) networks underlie lineage identity, but the role of these enhancers in intratumoral heterogeneity is unknown. Here we show that most neuroblastomas include two types of tumor cells with divergent gene expression profiles. Undifferentiated mesenchymal cells and committed adrenergic cells can interconvert and resemble cells from different lineage differentiation stages. ChIP-seq analysis of isogenic pairs of mesenchymal and adrenergic cells identified a distinct super-enhancer landscape and super-enhancer-associated TF network for each cell type. Expression of the mesenchymal TF PRRX1 could reprogram the super-enhancer and mRNA landscapes of adrenergic cells toward a mesenchymal state. Mesenchymal cells were more chemoresistant in vitro and were enriched in post-therapy and relapse tumors. Two super-enhancer-associated TF networks, which probably mediate lineage control in normal development, thus dominate epigenetic control of neuroblastoma and shape intratumoral heterogeneity.

Resistance to Epigenetic-Targeted Therapy Engenders Tumor Cell Vulnerabilities Associated with Enhancer Remodeling

“…We therefore profiled genome-wide distribution of H3K27Ac by ChIP-sequencing of JQ1 naive and resistant cells across both cell line models (Fig S3I-P). In concordance with previous studies, SE-associated genes: HAND1/2, GATA3, and PHOX2B , were identified in naive cells (Boeva et al, 2017; Chipumuro et al, 2014; van Groningen et al, 2017, Durbin et al, 2018). SE-marked genes and typical enhancer (TE)-marked genes, defined by high H3K27Ac signal in enhancer regions, were preferentially repressed by JQ1 (Figure S4A, B).…”

Anti‐tumor effects of PIM / PI 3K/ mTOR triple kinase inhibitor IBL ‐302 in neuroblastoma

“…Emerging data suggest that high‐risk neuroblastomas harbor a high degree of intratumor heterogeneity and contain tumor subclones with distinct genetic/epigenetic and/or phenotypic characteristics (Eleveld et al , ; Mengelbier et al , ; Schramm et al , ; Boeva et al , ; van Groningen et al , ; Braekeveldt et al , ; Karlsson et al , ). These findings suggest that general and/or combinatorial therapeutic strategies must be further explored.…”

Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma

“…Additionally, conservation of these proteins in cell lines implies their role as subtype MRs independent of stromal/immune infiltration. However, high rates of stromal and immune cell infiltration in a subset of these tumors suggests that single cell analysis may be required to further elucidate the interaction between tumor cells and stroma, including the presence of mesenchymal cells within neuroblastoma tumors highlighted by recent studies (86). Perhaps most importantly, identification of master regulator proteins responsible for the implementation and stability of high-risk neuroblastoma subtypes, which are conserved in cell-line models, provides the opportunity for the systematic identification of subtype-specific therapeutic vulnerabilities using methodologies such as OncoTreat, which were recently validated in neuroendocrine tumors (16).…”