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Series GSE54719 Query DataSets for GSE54719
Status Public on Jun 03, 2015
Title DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma [methylation]
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary 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.
Overall design Bisulphite converted DNA from the 35 neuroblastomas tumor, 2 ganglioneuromas and 4 non patological tissues ( 2 fetal brain and 2 adrenal gland) samples were hybridised to the Illumina Infinium HumanMethylation450K BeadChip
Contributor(s) Lavarino C
Citation(s) 26067621, 26484286
Submission date Feb 06, 2014
Last update date Jul 29, 2019
Contact name Cinzia Lavarino
Phone +34932804000
Organization name Hospital Sant Joan de Déu
Department Oncology
Lab Oncology
Street address Santa Rosa 39-57
City Esplugues de Llobregat
State/province Barcelona
ZIP/Postal code 08950
Country Spain
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (41)
GSM1322745 Reference1_AG1
GSM1322746 Reference2_AG2
GSM1322747 Reference3_FB1
This SubSeries is part of SuperSeries:
GSE54721 DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma.
BioProject PRJNA237498

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE54719_RAW.tar 183.1 Mb (http)(custom) TAR
GSE54719_non_normalized_meth.txt.gz 60.9 Mb (ftp)(http) TXT
GSE54719_non_normalized_unmeth.txt.gz 58.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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