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Promoter-wide profiling of DNA methylation in human neuroblastoma cells cultured with mood stabilizers.

ABSTRACT: Promoter-wide profiling of DNA methylation in human neuroblastoma cells cultured with mood stabilizers.

PROVIDER: PRJNA564943 | ENA |

REPOSITORIES: ENA

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Promoter-wide profiling of DNA methylation in human neuroblastoma cells cultured with mood stabilizers.

Project description:Bipolar disorder (BD) is a severe mental disorder characterized by repeated mood swings. Although genetic factors with small effect sizes are collectively associated with the pathophysiology of BD, the underlying molecular mechanisms, especially how environmental factors affect the brain genome, remain largely unknown. We revealed neuronal cell-type-specific, pathophysiology-related DNA methylation changes in the prefrontal cortex (PFC) of BD patients, highlighting the importance of the neural epigenome for understanding BD.

2021-04-09 | GSE137254 | GEO

CasID on RRM2 promoter region in neuroblastoma

Project description:dCas9-guided recruitment of the proximity ligation enzyme BirA* to the promoter region of RRM2 in SKNBE2c neuroblastoma cells.

2022-08-12 | PXD029630 | Pride

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers.

Project description:Accurate outcome prediction in neuroblastoma, which is necessary to enable the optimal choice of risk-related therapy, remains a challenge. To improve neuroblastoma patient stratification, this study aimed to identify prognostic tumor DNA methylation biomarkers.To identify genes silenced by promoter methylation, we first applied two independent genome-wide methylation screening methodologies to eight neuroblastoma cell lines. Specifically, we used re-expression profiling upon 5-aza-2'-deoxycytidine (DAC) treatment and massively parallel sequencing after capturing with a methyl-CpG-binding domain (MBD-seq). Putative methylation markers were selected from DAC-upregulated genes through a literature search and an upfront methylation-specific PCR on 20 primary neuroblastoma tumors, as well as through MBD- seq in combination with publicly available neuroblastoma tumor gene expression data. This yielded 43 candidate biomarkers that were subsequently tested by high-throughput methylation-specific PCR on an independent cohort of 89 primary neuroblastoma tumors that had been selected for risk classification and survival. Based on this analysis, methylation of KRT19, FAS, PRPH, CNR1, QPCT, HIST1H3C, ACSS3 and GRB10 was found to be associated with at least one of the classical risk factors, namely age, stage or MYCN status. Importantly, HIST1H3C and GNAS methylation was associated with overall and/or event-free survival.This study combines two genome-wide methylation discovery methodologies and is the most extensive validation study in neuroblastoma performed thus far. We identified several novel prognostic DNA methylation markers and provide a basis for the development of a DNA methylation-based prognostic classifier in neuroblastoma.

| S-EPMC3491423 | biostudies-literature

The Mood and Methylation Study (MMS)

Project description:The Mood and Methylation Study (MMS)

| PRJNA821589 | ENA

The Mood and Methylation Study (MMS)

Project description:The Mood and Methylation Study (MMS)

| PRJNA821591 | ENA

Promoter-wide profiling of DNA methylation in prefrontal cortex of Camk2-mutPolg mouse.

Project description:Camk2-mutPolg mouse carries the transgene of mutated polymerase gamma under Camk2 promoter. By the mutation, polymerase gamma lost its proof-reading activity, and thus tg mouse accumulates deletions and mutations in mitochondrial DNA in neurons. This mouse showed behavioral alterations similar to mood disorders. To examine the epigenetic status in the brain cells, we have performed promoter-wide DNA methylation analysis in neurons and nonneurons of the tg mouse.

2022-01-12 | GSE171120 | GEO

A genome wide methylation map of neuroblastoma cell lines

Project description:This SuperSeries is composed of the following subset Series: GSE31229: Neuroblastoma cell lines treated with DAC (2'-deoxy-5-azacytidine), a DNA-methylation inhibitor GSE31353: Methylation map of 8 neuroblastoma cell lines: NGS after MBD2-capture Refer to individual Series

2012-09-13 | E-GEOD-31355 | biostudies-arrayexpress

4C sequencing for the SOX11 promoter in the neuroblastoma cell lines CLB-GA, KELLY, SK-N-AS and SH-EP

Project description:4C sequencing for the SOX11 promoter in the neuroblastoma cell lines CLB-GA, KELLY, SK-N-AS and SH-EP.

2023-02-19 | E-MTAB-12580 | biostudies-arrayexpress

Genome-wide analysis of DNA methylation in neuroblastoma cell lines identifies MEGF10 as a novel epigenetically repressed tumour suppressor gene.

Project description:Background: Neuroblastoma is a childhood cancer in which many children still have poor outcomes, emphasising the need to better understand its pathogenesis. Despite recent genome-wide mutation analyses, most neuroblastomas do not contain recognisable driver mutations, suggesting that epigenetic changes could underlie many cases. Methods: To discover genes that become epigenetically deregulated during neuroblastoma tumorigenesis, we compared neuroblastomas to their neural crest precursor cells, using genome-wide DNA methylation analysis; probing CpG island promoter microarrays with methyl CpG-immunoprecipitated DNA. Results: We identified 93 genes that were significantly differently methylated between neuroblastoma cell lines and neural crest cells, of which 26 (28%) were hypermethylated and 67 (72%) were hypomethylated. Concentrating on hypermethylated genes to identify candidate tumour suppressor loci, we found the cell engulfment and adhesion factor gene MEGF10 to be epigenetically repressed by DNA hypermethylation or by H3K27/K9 methylation in neuroblastoma cell lines. MEGF10 showed significantly down-regulated expression in neuroblastoma tumour samples; furthermore patients with the lowest-expressing tumours had reduced relapse-free survival. Knock-down of MEGF10 expression in neuroblastoma cell lines promoted cell growth. Conclusion: Our results suggest that MEGF10 is a clinically relevant, epigenetically-deregulated neuroblastoma tumour suppressor.

2016-11-30 | GSE71958 | GEO

mTORC inhibition of neuroblastoma SK-N-BE(2)c cells cultured under hypoxic conditions

Project description:Differential expression of the oxygen sensitive hypoxia-inducible transcription factor (HIF) subunits HIF-1a and HIF-2a occurs in many tumor types, but the underlying regulatory mechanisms remain poorly understood. Here we investigate the role of mTOR complex in the regulation of HIF expression in cells cultured under hypoxic conditions. Neuroblastoma SK-N-BE(2)c cells were treated with DMSO or the mTORC complex inhibitor PP242 and cultured at hypoxia for 24, 48 or 72 hours.

2016-07-03 | E-GEOD-69833 | biostudies-arrayexpress

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