Genome-wide methylomic and transcriptomic analyses identify subtype-specific epigenetic signatures commonly dysregulated in GBM and GSCs

Genome-wide DNA methylation and trancription profiling of different subtypes in GBM (TCGA) and glioma stem cells (GSCs) were carried out using Illumina BeadChip HumanMethylation 450K array (450K array) to analyse over 485K CpG sites accross each samples. 450K array data for 94 GBM samples comprising 4 different subtypes i.e. Proneural (PN), Mesenchymal (MES), Classical (CL) and Neural (N) were used for GBM analysis. Similarly, 450K array for 23 GSCs and 1NHA, RNA seq for 29 GSCs and affimetrix microarray gene expression array for 12 GSCs were used for GBM data analyses. Bisulphite converted DNA from the for 23 GSCs and a NHA used used for Illumina Infinium 450k Human Methylation array.Differential methylation between the subtype(s) were carried out to generate subtype-specific DNA methylation signatues which were then compared to RNA seq and/or gene expression data.