Methylation Profiling Identifies Epigenetic Markers for High-grade Gliomas

Hypermethylation of CpG island is an epigenetic event prevalent in human gliomas. Here we employed a high-throughput microarray approach for a global search of DNA methylation to identify novel epigenetic loci in specific glioma subtypes. Hierarchical clustering analysis separated 20 glioma samples according to their WHO histopathological subtypes - pilocytic astrocytomas (PAs, grade I), oligoastrocytomas (OAs, grade II) and glioblastomas (GBMs, grade IV), based on their unique methylation patterns. The overall methylation frequency of the low-grade PAs was significantly less than that of the more aggressive OAs and GBMs (0.45% versus 2.0% and 1.4%; PAs versus OAs, p<0.01; PAs versus GBMs, p<0.01). The lower level of DNA methylation observed in PAs may be in part due to the increased methylation of multiple CpG islands which occur in more advanced tumors. However, the young age of onset of PAs may also contribute to this observed difference. Although there were many hypermethylated loci exclusive to the OA and GBM subtypes, the methylation frequencies between these groups were not significantly different. Analysis by methylation-specific PCR on an expanded set of samples and on more glioma subtypes further confirmed an epigenetic marker, SMARCA5, the hypermethylation of which was preferentially observed in grade IV, but not in grades I or II gliomas (p<0.0001). The intermediate grade III gliomas showed low levels of SMARCA5 hypermethylation. Epigenetic loci uncovered in the present study recapitulate the histopathological differences of these gliomas, indicating that these molecular changes may be responsible for the development of the different glioma subtypes. On-going work in our laboratory has shown that some of these loci are indeed hypermethylated in the early stages of astrocytic tumors.