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Series GSE21714 Query DataSets for GSE21714
Status Public on Jan 01, 2011
Title Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Aberrant DNA methylation (DNAm) was first linked to cancer over 25 years ago. Since then, many studies have associated hypermethylation of tumour suppressor genes and hypomethylation of oncogenes to the tumourigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs). Recently, new technologies for whole-genome DNAm (methylome) analysis have been developed, enabling unbiased analysis of cancer methylomes. Using MeDIP-seq, we report a sequencing-based comparative methylome analysis of malignant peripheral nerve sheath tumours (MPNST), benign Neurofibromas and normal Schwann cells. Analysis of these methylomes revealed a complex landscape of DNAm alterations. Contrary to the current dogma, significant global hypomethylation was not observed in the MPNST methylome. However, a highly significant (P<10-100) directional difference in DNAm was found in satellite repeats, suggesting these repeats to be the main target for hypomethylation in MPNST. Comparative analysis of the MPNST and Schwann cell methylomes identified 101,466 cancer-associated differentially methylated regions (cDMRs). Analysis showed these cDMRs to be significantly enriched for two satellite repeat types (SATR1 and ARLĪ±) and suggests an association between aberrant DNAm of these sequences and transition from healthy cells to malignant disease. Significant enrichment of hypermethylated cDMRs in CGI shores (P<10-60), non-CGI-associated promoters (P<10-4) and hypomethylated cDMRs in SINE repeats (P<10-100) was also identified. Integration of DNAm and gene expression data showed that the expression pattern of genes associated with CGI shore cDMRs was able to discriminate between disease phenotypes. This study establishes MeDIP-seq as an effective method to analyse cancer methylomes.
 
Overall design Examination of methylation profiles in malignant, benign and normal tissue
 
Contributor(s) Feber A, Wilson G, Zhang L, Presneau N, Idowu B, Down TA, Rakyan VK, Stupka E, Teschendorff AE, Schroth G, Flanagan A, Beck S
Citation(s) 21324880
Submission date May 06, 2010
Last update date May 15, 2019
Contact name Gareth Wilson
E-mail gareth.wilson@ucl.ac.uk
Organization name UCL Cancer Institute
Street address 23 Huntley Street
City London
ZIP/Postal code WC1E 6BT
Country United Kingdom
 
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (3)
GSM541729 MPNST MeDIP-seq
GSM541730 Benign neurofibroma MeDIP-seq
GSM541731 Schwann cell MeDIP-seq
Relations
SRA SRP002434
BioProject PRJNA127151

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
GSE21714_RAW.tar 24.2 Gb (http)(custom) TAR (of BAM, GFF)
Processed data provided as supplementary file
Raw data are available in SRA

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