Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries

Abstract

Neuroblastoma is a tumor of the peripheral sympathetic nervous system, derived from multipotent neural crest cells (NCCs). To define core regulatory circuitries (CRCs) controlling the gene expression program of neuroblastoma, we established and analyzed the neuroblastoma super-enhancer landscape. We discovered three types of identity in neuroblastoma cell lines: a sympathetic noradrenergic identity, defined by a CRC module including the PHOX2B, HAND2 and GATA3 transcription factors (TFs); an NCC-like identity, driven by a CRC module containing AP-1 TFs; and a mixed type, further deconvoluted at the single-cell level. Treatment of the mixed type with chemotherapeutic agents resulted in enrichment of NCC-like cells. The noradrenergic module was validated by ChIP-seq. Functional studies demonstrated dependency of neuroblastoma with noradrenergic identity on PHOX2B, evocative of lineage addiction. Most neuroblastoma primary tumors express TFs from the noradrenergic and NCC-like modules. Our data demonstrate a previously unknown aspect of tumor heterogeneity relevant for neuroblastoma treatment strategies.

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.…”

Event‐free survival of infants and toddlers enrolled in the HR‐NBL‐1/SIOPEN trial is associated with the level of neuroblastoma mRNAs at diagnosis

“…Although the expression of the three NB mRNAs correlated to each other, the combination of TH and PHOX2B mRNAs in BM increased the prognostic performance of either alone. This may be due to the limited number of study subjects or may reflect differences in the expression of TH and PHOX2B mRNAs in the neoplastic cells, which will require further studies in additional cohorts. In PB, PHOX2B mRNA significantly dichotomized the prognosis of the study cohort, identifying 23 (34%) patients with poor outcome (5‐year EFS = 29%, 95% CI: 12–48%).…”

“…Furthermore, the combination of high TH and PHOX2B mRNAs in BM for 23% of the study cohort was significantly associated with a poor outcome (5- Although the expression of the three NB mRNAs correlated to each other, the combination of TH and PHOX2B mRNAs in BM increased the prognostic performance of either alone. This may be due to the limited number of study subjects or may reflect differences in the expression of TH and PHOX2B mRNAs in the neoplastic cells, 21,22 which will require further studies in additional cohorts. In PB, PHOX2B 23 and advocating separate investigations of right and left BM aspirates.…”

“…25,26 In PB, the levels of PHOX2B and DCX mRNA that dichotomize infants was close to the previously defined cut-points (0.07 vs. 0.28, and 0.16 vs. 0.41, respectively 14 ), whereas TH mRNA levels in blood were not predictive of outcome. This may be related to either expression of TH mRNA in more differentiated, sympathetic-committed neuronal cells 21,22,24 or to its reported illegitimate transcription. 24,[27][28][29][30][31][32] Taken together, the differences observed in NB mRNAs in infants/toddlers, as compared to children, 14 may be linked to their better outcome.…”