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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

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 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

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

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 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

RRBS-based quantitative methylation analysis define 100% methylation fidelity CpG sites

Project description:Stable maintenance of cytosine methylation is essential for mammalian biological processes such as gene transcription. This study introduced a RRBS-based quantitative method to identify CpG sites of high methylation fidelity (especially those 100% methylation fidelity sites). To separate the 100% methylation fidelity sites , we cultured the ARPE-19, Jurkat and SW1353 cells for lasting 10 generations, and we detected the methylation level of each CpG sites in the 20th generation and the 30th generation by performing reduced representation bisulfite sequencing (RRBS), to obtain the 100% methylation fidelity sites. The result shows that the number of overlapped fidelity methylation CpG sites of the two different time is smaller than number of each generation. Our results also showed that the proportion of high-fidelity 100% methylated sites in Jurkat and ARPE-19 cells is about 4.4% and 8.9%, and the proportion in SW1353 cells is 1.98%. The fidelity methylation sites obtained by the comparison of the two different time periods are the truly unchanged CpG sites during cell passage, which improves the reliability of the fidelity methylation sites. In summary, we provide new insights into the DNA methylation fidelity study.

2021-06-08 | GSE176335 | GEO

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 DNA of 15 primary stage 4S 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

2015-12-15 | E-GEOD-69268 | biostudies-arrayexpress

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