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| 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 [gene expression] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| 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.
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| Overall design |
RNA from 20 neuroblastoma tumor and 4 non patological tissues (2 fetal brain and 2 adrenal gland) samples were hybridised to the Affymetrix Human Genome U219- 24array plate.
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| Contributor(s) |
Lavarino C |
| Citation(s) |
26067621, 26484286 |
| Submission date |
Feb 06, 2014 |
| Last update date |
Jul 29, 2019 |
| Contact name |
Cinzia Lavarino |
| E-mail(s) |
clavarino@fsjd.org
|
| Phone |
+34932804000
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| 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 |
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| Platforms (1) |
| GPL13667 |
[HG-U219] Affymetrix Human Genome U219 Array |
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| Samples (23)
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| 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. |
|
| Relations |
| BioProject |
PRJNA237499 |
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