DNA methylation analysis of paediatric pilocytic and diffuse astrocytomas

Paediatric low-grade gliomas (LGGs) account for about a third of all brain tumours in children. We conducted a detailed study of DNA methylation to improve our understanding of the biology of pilocytic and diffuse astrocytomas. Comparisons were performed between tumours and normal brain controls from matching location, and between pilocytic and diffuse astrocytomas. Pilocytic astrocytomas were found to have a distinctive signature involving 315 CpG sites, with the majority of the sites (312 CpG sites) hypomethylated in pilocytic astrocytomas. Additionally many of the sites were located within annotated enhancers. The distinct signature in pilocytic astrocytomas was not present in diffuse astrocytomas or in published profiles of other brain tumours and normal brain tissue. On further analysis of the 315 CpG sites, the AP-1 transcription factor complex was predicted to bind within 200bp of a subset of teh 315 differentially methylated CpG sites. We also observed up-regulation of the AP-1 factors, FOS and FOSL1 in pilocytic astrocytomas. Our findings highlight novel epigenetic differences between pilocytic and diffuse astrocytomas, in addition to well-described alterations involving BRAF, MYB and FGFR1. Genomic DNA from frozen tumour material was bisulphite converted and analysed using Illumina Infinium HumanMethylation 450K arrays. Pre-processing was performed using genome studio. Statistical approaches were used to identify differential methylation patterns between 17 pilocytic astrocytoma, 10 diffuse astrocytoma and normal brain controls (1 foetal brain, 1 adult brain, 1 foetal cerebellum, 1 foetal frontal lobe and ReN VM Neural Stem Cell-line).