Intrinsic transcriptional heterogeneity in neuroblastoma guides mechanistic and therapeutic insights

Shendy, Noha A.M.; Zimmerman, Mark W.; Abraham, Brian J.; Durbin, Adam D.

doi:10.1016/j.xcrm.2022.100632

Cited by 18 publications

(32 citation statements)

References 93 publications

(210 reference statements)

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“…Neuroblastoma tumors are highly heterogeneous, and comprise both adrenergic and neural crest like (mesenchymal) cell types. Both cell identities are charactized by super-enhancer marked transcription factors, which are controlling the gene expression program of the two neuroblastoma cell identities 45 . In contract, genes involved in replication and replication stress response pathways comprising FANCD2, CDC25A, CHEK1 and AURKA are downregulated ( Figure 5B ).…”

Section: Resultsmentioning

confidence: 99%

“…Enrichment analysis using ENRICHR 29 on the overlapping binding sites in CLB-GA showed again significant enrichment for binding sites of the ADR CRC transcription factors ( Figure 6E) . As these CRC members are known to be highly transcribed in neuroblastoma, these regions are inherently at higher risk to suffer from replicative stress 45 . Therefore, we propose that PHF6 is recruited to these regions and attracts RRM2 to relief transcription-associated DNA damage.…”

Section: Resultsmentioning

confidence: 99%

“…The 730 common upregulated included amongst others GATA2, GATA3 and HAND2. Interestingly, along with PHOX2B, ASCL1, TBX2, ISL1 and others, these are members of the previously described adrenergic neuroblastoma 'core regulatory circuitry' (CRC) [43][44][45] . Neuroblastoma tumors are highly heterogeneous, and comprise both adrenergic and neural crest like (mesenchymal) cell types.…”

Section: Knockdown Of Phf6 In Neuroblastoma Cell Lines Leads To Incre...mentioning

confidence: 92%

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The fork restart factor PHF6 interacts with RRM2 and binds to H3K56ac marked nascent DNA

Depestel

Sanders

Bekaert

et al. 2023

Preprint

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The plant homeodomain zinc finger protein 6 (PHF6) is affected by germline mutations in patients with cognitive disabilities and somatic mutations in acute T-cell leukemia (T-ALL). We and others previously obtained evidence for a key role of PHF6 in hematopoietic precursor cell self-renewal capacity and lineage commitment during differentiation, while recent work revealed a role in non-homologous end joining and G2 checkpoint recovery. In this study, we identified the ribonucleotide reductase subunit M2 (RRM2), as a novel PHF6 interacting protein by immunoprecipitation coupled mass spectrometry. We confirmed the PHF6-RRM2 interaction in different normal and malignant cellular background and mapped the interaction interface towards the first PHD domain of PHF6 through NanoBRET based deletion mapping. We also demonstrated that PHF6 knockdown in neuroblastoma cells causes increased replicative stress and DNA damage. Furthermore, we show binding of PHF6 to the DNA-damage associated H3K56ac histone mark. In view of our recent finding of RRM2 as a MYCN co-dependency and target for synergistic CHK1 inhibition in neuroblastoma, we performed CUT&RUN mapping of H3K56ac and PHF6 genome-wide binding sites in neuroblastoma cells and next to a significant overlap of the two, we also found evidence for a functional crosstalk with established core regulatory circuitry transcription factors. Our data suggest that PHF6 is a component of the earlier proposed replitase, implicated in active regulation of RRM2 function during replication and DNA repair.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Knockdown Of Phf6 In Neuroblastoma Cell Lines Leads To Incre...mentioning

confidence: 92%

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The fork restart factor PHF6 interacts with RRM2 and binds to H3K56ac marked nascent DNA

Depestel

Sanders

Bekaert

et al. 2023

Preprint

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“…This is similar to the idea of the epithelial to mesenchymal transition (EMT) states. However, while neuroblastoma cells can be classified as either in the MES or ADRN state, sufficient plasticity exists where transitioning between states could also cause transcriptional changes that are independent of the cell’s mutational status ( 46 ). Expanded complexity of transcriptional networks is exemplified with MES subtypes that can include both MYCN -amplified and nonamplified, high-risk or low-risk, and may also overlap with the ADRN group ( 47 ).…”

Section: Discussionmentioning

confidence: 99%

Chaperonin containing TCP-1 (CCT/TRiC) is a novel therapeutic and diagnostic target for neuroblastoma

et al. 2022

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Chaperonin containing TCP1 (CCT/TRiC) is a multi-subunit protein folding complex that enables the cancer phenotype to emerge from the mutational landscape that drives oncogenesis. We and others linked increased expression of CCT subunits to advanced tumor stage and invasiveness that inversely correlates with cancer patient outcomes. In this study, we examined the expression of the second CCT subunit, CCT2, using genomic databases of adult and pediatric tumors and normal tissues, and found that it was highly expressed in pediatric cancers, showing a significant difference compared to normal tissues. Histologic staining confirmed that CCT subunits are highly expressed in tumor tissues, which was exemplified in neuroblastoma. Using two neuroblastoma cells, MYCN-amplified, IMR-32 cells, and non-amplified, SK-N-AS cells, we assessed baseline levels for CCT subunits and found expressions comparable to the highly invasive triple-negative breast cancer (TNBC) cell line, MDA-MB-231. Exogenous expression of CCT2 in both SK-N-AS and IMR-32 cells resulted in morphological changes, such as larger cell size and increased adherence, with significant increases in the CCT substrates, actin, and tubulin, as well as increased migration. Depletion of CCT2 reversed these effects and reduced cell viability. We evaluated CCT as a therapeutic target in IMR-32 cells by testing a novel peptide CCT inhibitor, CT20p. Treatment with CT20p induced cell death in these neuroblastoma cells. The use of CCT2 as a biological indicator for detection of neuroblastoma cells shed in blood was examined by spiking IMR-32 cells into human blood and using an anti-CCT2 antibody for the identification of spiked cancer cells with the CellSearch system. Results showed that using CCT2 for the detection of neuroblastoma cells in blood was more effective than the conventional approach of using epithelial markers like cytokeratins. CCT2 plays an essential role in promoting the invasive capacity of neuroblastoma cells and Frontiers in Oncology frontiersin.org 01

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“…However, this represents an apparent paradox, because the mesenchymal cell state appears to be associated both with the initiation of localized tumors in young children and with rapidly growing and metastatic drug resistant neuroblastomas that are not responding to therapy. To explain this apparent discrepancy, we hypothesize that adrenergic neuroblastoma cells can both switch to the mesenchymal cell state and 20 select for RAS-MAPK pathway mutations under the pressure of intensive combination chemotherapy (6,11,(43)(44)(45)(46)(47). Thus, the switch to the mesenchymal cell state provides immediate resistance to anti-neuroblastoma drugs but relatively indolent cell growth, allowing for the long term outgrowth of rare subclones of cells with drug resistance due to RAS-MAPK pathway mutations, and impart aggressive proliferative and metastatic growth properties, which may allow the neuroblastoma cells to shift back to the adrenergic cell state.…”

Section: The Tata/tata Genotype At Rs2168101 Favors the Onset Of Neur...mentioning

confidence: 99%

Genetic Predisposition to Neuroblastoma Results from a Regulatory Polymorphism that Promotes the Adrenergic Cell State

Weichert-Leahey

Shi

Tao

et al. 2023

Preprint

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Childhood neuroblastomas exhibit plasticity between an undifferentiated neural crest-like “mesenchymal” cell state and a more differentiated sympathetic “adrenergic” cell state. These cell states are governed by autoregulatory transcriptional loops called core regulatory circuitries (CRCs), which drive the early development of sympathetic neuronal progenitors from migratory neural crest cells during embryogenesis. The adrenergic cell identity of neuroblastoma requires LMO1 as a transcriptional co-factor. Both LMO1 expression levels and the risk of developing neuroblastoma in children are associated with a single nucleotide polymorphism G/T that affects aGATA motif in the first intron of LMO1. Here we show that wild-type zebrafish with theGATA genotype develop adrenergic neuroblastoma, while knock-in of the protectiveTATA allele at this locus reduces the penetrance of MYCN-driven tumors, which are restricted to the mesenchymal cell state. Whole genome sequencing of childhood neuroblastomas demonstrates thatTATA/TATA tumors also exhibit a mesenchymal cell state and are low risk at diagnosis. Thus, conversion of the regulatoryGATA to aTATA allele in the first intron ofLMO1reduces the neuroblastoma initiation rate by preventing formation of the adrenergic cell state, a mechanism that is conserved over 400 million years of evolution separating zebrafish and humans.

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Intrinsic transcriptional heterogeneity in neuroblastoma guides mechanistic and therapeutic insights

Cited by 18 publications

References 93 publications

The fork restart factor PHF6 interacts with RRM2 and binds to H3K56ac marked nascent DNA

The fork restart factor PHF6 interacts with RRM2 and binds to H3K56ac marked nascent DNA

Chaperonin containing TCP-1 (CCT/TRiC) is a novel therapeutic and diagnostic target for neuroblastoma

Genetic Predisposition to Neuroblastoma Results from a Regulatory Polymorphism that Promotes the Adrenergic Cell State

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