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Epigenetic state determines inflammatory sensing in neuroblastoma [ATAC-seq]

ABSTRACT: Epigenetic state determines inflammatory sensing in neuroblastoma [ATAC-seq]

PROVIDER: PRJNA754359 | ENA |

REPOSITORIES: ENA

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Epigenetic state determines inflammatory sensing in neuroblastoma

Project description:Epigenetic state determines inflammatory sensing in neuroblastoma

| PRJNA754370 | ENA

Epigenetic state determines inflammatory sensing in neuroblastoma [RNA-seq]

Project description:Epigenetic state determines inflammatory sensing in neuroblastoma [RNA-seq]

| PRJNA754375 | ENA

Epigenetic state determines inflammatory sensing in neuroblastoma [ATAC-seq]

Project description:Immunotherapy has revolutionized cancer treatment, but many cancers are not impacted by currently available immunotherapeutic strategies. Here, we investigated inflammatory signaling pathways in neuroblastoma, a classically “cold” pediatric cancer. By testing the functional response of a panel of 20 diverse neuroblastoma cell lines to three different inflammatory stimuli, we found that all cell lines have intact interferon signaling and all but one lack functional cytosolic DNA sensing via cGAS-STING. However, dsRNA sensing via TLR3 was heterogeneous, as was signaling through other dsRNA sensors and TLRs more broadly. Seven cell lines showed robust response to dsRNA, six of which are in the mesenchymal epigenetic state, while all unresponsive cell lines are in the adrenergic state. Genetically switching adrenergic cell lines towards the mesenchymal state fully restored responsiveness. In responsive cells, dsRNA sensing results in the secretion of pro-inflammatory cytokines, enrichment of inflammatory transcriptomic signatures, and increased tumor killing by T cells in vitro. Using single cell RNA sequencing data, we show that human neuroblastoma cells with stronger mesenchymal signatures have a higher basal inflammatory state, demonstrating intra tumoral heterogeneity in inflammatory signaling that has significant implications for immunotherapeutic strategies in this aggressive childhood cancer.

2022-01-22 | GSE182041 | GEO

Epigenetic state determines inflammatory sensing in neuroblastoma [RNA-seq]

2022-01-22 | GSE182051 | GEO

Epigenetic state determines inflammatory sensing in neuroblastoma

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-01-21 | GSE182052 | GEO

MPTAC determines APP fragmentation via sensing sulfur amino acid catabolism

Project description:MPTAC determines APP fragmentation via sensing sulfur amino acid catabolism

| PRJNA453384 | ENA

Metabolic state determines drug response in liver cancer

Project description:Metabolic state determines drug response in liver cancer

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Distinct SOX signature determines neuroblastoma origin and predicts clinical outcome

Project description:Distinct SOX signature determines neuroblastoma origin and predicts clinical outcome

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

Project description: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 a GATA motif in the first intron of LMO1. Here we showed that wild-type zebrafish with the GATA genotype developed adrenergic neuroblastoma, while knock-in of the protective TATA allele at this locus reduced the penetrance of MYCN-driven tumors, which were restricted to the mesenchymal cell state. Whole genome sequencing of childhood neuroblastomas demonstrated that TATA/TATA tumors also exhibited a mesenchymal cell state and were low risk at diagnosis. Thus, conversion of the regulatory GATA to a TATA allele in the first intron of LMO1 reduced the neuroblastoma initiation rate by preventing formation of the adrenergic cell state, a mechanism that was conserved over 400 million years of evolution separating zebrafish and humans.

2023-04-25 | GSE224158 | GEO

Network-based, cross-cohort discovery of transcriptional mechanisms presiding over maintenance of high-risk neuroblastoma subtype state

Project description:Network-based analysis of neuroblastoma samples from two large cohorts identified master regulator proteins controlling the transcriptional state of three high-risk molecular subtypes. In particular, a TEAD4-MYCN positive feedback loop emerged as the core regulatory motif of a small protein module presiding over implementation and stability of the subtype associated with MYCN amplification. Specifically, MYCN transcriptionally activates TEAD4, which in turn activates MYCN both transcriptionally and post-translationally. The resulting MYCN-TEAD4 positive feedback loop plays a critical role in maintaining aberrant activity of a 10-protein regulatory module that causally regulates the transcriptional state of this subtype. Consistently, loss of TEAD4 activity induces core module activity collapse and abrogates neuroblastoma cell viability in vitro and in vivo, thus suggesting novel therapeutic strategies for this important childhood cancer. Study of the transcriptional control by TEAD4 and MYCN positive feedback loop using RNA-seq profiles of TEAD4 and MYCN shRNA knockdowns in neuroblastoma BE2 cells. ChIP-Seq analysis using TEAD4 antibody in BE2 cells.

2016-07-18 | E-GEOD-84389 | biostudies-arrayexpress

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