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DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma.

ABSTRACT: DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma.

PROVIDER: PRJNA237496 | ENA |

REPOSITORIES: ENA

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DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma [methylation]

Project description:DNA methylation changes in neuroblastoma, a clinically-heterogeneous pediatric tumor, have been described essentially in promoter regions. We analyzed the DNA methylome of neuroblastoma using high-density microarrays and observed differential methylation not only in promoters but also in intragenic and intergenic regions at both CpG and non-CpG sites. These epigenetic changes showed a non-random distribution relative functional chromatin domains, and targeted development and cancer-related genes, relevant for neuroblastoma pathogenesis. CCND1, a gene overexpressed in neuroblastoma, showed hypomethylation of gene-body and upstream regulatory regions. Furthermore, tumors with diverse clinical-risk showed clear differences affecting CpG and, remarkably, non-CpG sites. Non-CpG methylation was present in clinically-favorable tumors and affected genes such as ALK, where non-CpG methylation correlated with low gene expression. Finally, we identified CpG and non-CpG methylation signatures which correlated with patient’s age at time-points relevant for neuroblastoma clinical behavior, and targeted genes related to neural development and neural crest regulatory network We report on the first DNA methylomes of neuroblastoma tumors using high-density microarrays. DNA methylation changes in this pediatric tumor affected both CpG and non-CpG sites associated with developmental and cancer-related genes such as CCND1 and ALK. Our study also provides new insights into the molecular basis of the heterogeneous clinical behavior of neuroblastoma.

2015-06-03 | GSE54719 | GEO

DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma [gene expression]

2015-06-03 | GSE54720 | GEO

Methyl-CpG-binding domain (MBD) sequencing of 45 primary neuroblastoma tumors

Project description:The DNA methylome of 45 primary neuroblastoma tumors is profiled by enrichment with a methyl-CpG-binding domain (MBD) and massively parallel sequencing

2015-11-19 | GSE69243 | GEO

Methyl-CpG-binding domain (MBD) sequencing of 42 primary neuroblastoma tumors

Project description:The DNA methylome of 42 primary neuroblastoma tumors is profiled by enrichment with a methyl-CpG-binding domain (MBD) and massively parallel sequencing

2015-11-19 | GSE69224 | GEO

DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma.

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

2015-06-03 | GSE54721 | GEO

Methyl-CpG-binding domain (MBD) sequencing of neuroblastoma tumors

Project description:Methyl-CpG-binding domain (MBD) sequencing of neuroblastoma tumors

| PRJNA285076 | ENA

Methyl-CpG-binding domain (MBD) sequencing of 15 primary stage 4S neuroblastoma tumors

Project description:The DNA methylome of 15 primary stage 4S neuroblastoma tumors is profiled by enrichment with a methyl-CpG-binding domain (MBD) and massively parallel sequencing

2015-12-15 | GSE69268 | GEO

Homo sapiens

Project description:DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma [methylation]

| PRJNA237498 | ENA

Homo sapiens

Project description:DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma [gene expression]

| PRJNA237499 | ENA

Methyl-CpG-binding domain (MBD) sequencing of 45 primary neuroblastoma tumors

Project description:The DNA methylome of 45 primary neuroblastoma tumors is profiled by enrichment with a methyl-CpG-binding domain (MBD) and massively parallel sequencing DNA of 45 primary tumors is sheared (fragments of Â± 200 bp), followed by MBD-based (MethylCap kit of Diagenode) enrichement, library preparation and multiplexing. Both input DNA and captured DNA were sequenced paired-end on Illumina Hiseq2000

2015-11-19 | E-GEOD-69243 | biostudies-arrayexpress

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