Epigenetic deregulation of GATA3 in neuroblastoma is associated with increased GATA3 protein expression and with poor outcomes

Abstract

To discover epigenetic changes that may underly neuroblastoma pathogenesis, we identified differentially methylated genes in neuroblastoma cells compared to neural crest cells, the presumptive precursors cells for neuroblastoma, by using genome-wide DNA methylation analysis. We previously described genes that were hypermethylated in neuroblastoma; in this paper we report on 67 hypomethylated genes, which were filtered to select genes that showed transcriptional over-expression and an association with poor prognosis in neuroblastoma, highlighting GATA3 for detailed studies. Specific methylation assays confirmed the hypomethylation of GATA3 in neuroblastoma, which correlated with high expression at both the RNA and protein level. Demethylation with azacytidine in cultured sympathetic ganglia cells led to increased GATA3 expression, suggesting a mechanistic link between GATA3 expression and DNA methylation. Neuroblastomas that had completely absent GATA3 methylation and/or very high levels of protein expression, were associated with poor prognosis. Knock-down of GATA3 in neuroblastoma cells lines inhibited cell proliferation and increased apoptosis but had no effect on cellular differentiation. These results identify GATA3 as an epigenetically regulated component of the neuroblastoma transcriptional control network, that is essential for neuroblastoma proliferation. This suggests that the GATA3 transcriptional network is a promising target for novel neuroblastoma therapies.

Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes

“…The largest such coefficient in the gene-wide GATA3 task trained on METABRIC-(LumA) belonged to MEGF10 (Additional file 3 : Figure S2), which has been previously implicated in cancer processes downstream of GATA3 [ 45 ]. MEGF10 was also weighted heavily in the best found subgrouping task, having the 37th largest absolute magnitude out of 13018 genes considered by the model.…”

Development and Carcinogenesis: Roles of GATA Factors in the Sympathoadrenal and Urogenital Systems

“…In these neuroblastoma cell lines, the DNA methylation level of the GATA3 gene locus was lower than that in normal human neural crest cells [32]. Subsequent analysis of clinical relevance revealed that high GATA3 expression tended to be associated with poor prognosis, indicating a close correlation between GATA3 expression levels and the clinical properties of neuroblastomas [32]. As an-ticipated, GATA3 siRNA (small interfering RNA) knockdown in neuroblastoma cell lines inhibited proliferation and increased apoptosis [31].…”

“…Recent genome-wide studies have characterized broad alterations in DNA methylation status in a series of neuroblastoma cell lines [31]. In these neuroblastoma cell lines, the DNA methylation level of the GATA3 gene locus was lower than that in normal human neural crest cells [32]. Subsequent analysis of clinical relevance revealed that high GATA3 expression tended to be associated with poor prognosis, indicating a close correlation between GATA3 expression levels and the clinical properties of neuroblastomas [32].…”

The sympathies of the body: functional organization and neuronal differentiation in the peripheral sympathetic nervous system

“…Analysis of the action of neuroblastoma PHOX2b variants in developing sympathetic neurons demonstrated their stimulatory effect on neuroblast proliferation combined with dedifferentiation indicating routes to malignancy modulated by PHOX2b in combination with HAND2 (Reiff et al 2010 ). Studies for other transcription factors of the network directing sympathetic neuron differentiation and their role in neuroblastoma exist for GATA3 (Almutairi 2019 ; Moriguchi 2021 ) and ASCL1 (Wang et al 2019 ; Ali et al 2020 ).…”