DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas.

Jennie N Jeyapalan,Steven C Clifford,Tania A Jones,Alexander Tep,Edward C Schwalbe,Denise Sheer,Gabriel T Doctor,Samuel N Alberman,Magdalena Lecain,Chirag M Haria,Alfred A Hill,Diego Ottaviani,Ibrahim Qaddoumi,Ruth G Tatevossian,David W Ellison,Isabel C F Morley

doi:10.1186/s40478-016-0323-6

Abstract

Low-grade gliomas (LGGs) account for about a third of all brain tumours in children. We conducted a detailed study of DNA methylation and gene expression to improve our understanding of the biology of pilocytic and diffuse astrocytomas. Pilocytic astrocytomas were found to have a distinctive signature at 315 CpG sites, of which 312 were hypomethylated and 3 were hypermethylated. Genomic analysis revealed that 182 of these sites are within annotated enhancers. The signature was not present in diffuse astrocytomas, or in published profiles of other brain tumours and normal brain tissue. The AP-1 transcription factor was predicted to bind within 200 bp of a subset of the 315 differentially methylated CpG sites; the AP-1 factors, FOS and FOSL1 were found to be up-regulated in pilocytic astrocytomas. We also analysed splice variants of the AP-1 target gene, CCND1, which encodes cell cycle regulator cyclin D1. CCND1a was found to be highly expressed in both pilocytic and diffuse astrocytomas, but diffuse astrocytomas have far higher expression of the oncogenic variant, CCND1b. These findings highlight novel genetic and epigenetic differences between pilocytic and diffuse astrocytoma, in addition to well-described alterations involving BRAF, MYB and FGFR1.Electronic supplementary materialThe online version of this article (doi:10.1186/s40478-016-0323-6) contains supplementary material, which is available to authorized users.

Highlights

Pilocytic astrocytomas (WHO grade I) constitute the majority of paediatric low-grade gliomas (LGGs)
Identification of a hypomethylation signature specific to pilocytic astrocytomas DNA methylation profiles were identified for the test tumour set (11 infratentorial pilocytic astrocytomas; 6 supratentorial pilocytic astrocytomas and 10 diffuse astrocytomas), 4 normal brain control samples and the ReN VM neural stem cell-line using the Illumina Infinium HumanMethylation450 BeadChip [3, 8]
In summary, pilocytic astrocytomas contain a hypomethylation signature characterised by CpG sites which are located predominantly in annotated enhancers

Summary

Introduction

Pilocytic astrocytomas (WHO grade I) constitute the majority of paediatric low-grade gliomas (LGGs). They usually arise in the cerebellum but are found in other sites such as the optic pathways and cerebral hemispheres. We have conducted a comprehensive analysis of DNA methylation together with gene expression in pilocytic and diffuse astrocytomas from two independent tumour sets (test set n = 27 and validation set n = 59) using the Illumina HumanMethylation450 BeadChip (450K). We identified a hypomethylation signature specific to pilocytic astrocytomas, characterised by differentially methylated CpG sites predominantly in annotated enhancers. The FOS family of transcription factors was found to be up-regulated in pilocytic astrocytomas. The AP-1 gene target CCND1a was upregulated in both pilocytic and diffuse astrocytomas, with higher levels of the oncogenic CCND1b transcript expressed in the diffuse astrocytomas

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Conclusion