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

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.

Integrated DNA methylation analysis identifies topographical and tumoral biomarkers in pilocytic astrocytomas

“…The differentially expressed genes identified by Sharma and colleagues [ 16 ] are implicated in the development of the forebrain and the hindbrain. One of these genes, IRX2 , was found differentially expressed [ 16 , 18 , 20 ] and differentially methylated between infratentorial and supratentorial PAs in our and other studies [ 5 , 20 ]. In particular, Jeyapalan et al [ 20 ] identified an intergenic CpG site associated to IRX2 that resulted to be differentially methylated between the two tumor groups; whereas we detected a differential methylation of a CpG island that spans the promoter region and part of the gene body of IRX2 .…”

“…This finding was supported by the identification of distinct gene expression [ 5 , 15 – 20 ] and methylation profiles [ 5 , 20 , 21 ] between tumors having different localizations. Sharma et al [ 16 ] described a specific gene expression pattern discriminating infratentorial and supratentorial PAs.…”

Advances in the classification of pediatric brain tumors through DNA methylation profiling: From research tool to frontline diagnostic

“…Furthermore, intracranial (nongerminomatous) germ cell tumors will require careful evaluation by this method because of inherent variability in the contribution and composition of teratomatous elements, the often substantial stromal contribution to the tumor, and the often focal nature of malignant germ cell tumor elements. 85,86 For rare tumor types or tumors that present with challenging histomorphology, methylation-based approaches will allow for better standardization of diagnoses across centers. As discussed, tumor subgrouping and subtyping based on methylation profiling are expected to improve prognostication, risk assignment, and treatment stratification.…”

“…Classification by methylation profiling may be impossible in cases with insufficient biopsy tissue or poor DNA yields. Hypocellular low‐grade tumors or those with stromal contamination may not contain sufficient tumoral DNA to yield an accurate classification, as is the case for some diffuse astrocytomas . Even in cases with adequate material, some tumors may remain unclassifiable by methylation, as observed in a recent comprehensive cohort with 82 methylation classes in which approximately 12% of samples scored too poorly for confident classification .…”

“…Further work also will be needed to validate DNA methylation profiling for classifying LGG, due to frequent difficulty in class assignment. Furthermore, intracranial (nongerminomatous) germ cell tumors will require careful evaluation by this method because of inherent variability in the contribution and composition of teratomatous elements, the often substantial stromal contribution to the tumor, and the often focal nature of malignant germ cell tumor elements …”