Abstract 4724: Identification of a CpG-island methylator phenotype (CIMP) in a subgroup of pilocytic astrocytoma with favorable prognosis

Pilocytic astrocytomas (PA) are classified as WHO grade I tumors, and comprise the most frequent brain tumor in childhood. The most common tumor location is the cerebellum, and these tumors can typically be completely resected. However, for tumors in other locations such as the diencephalon, brain stem, or optic tract, complete tumor resection is often challenging. Recently, we were able to identify BRAF as a centrally important oncogene in these tumors, showing duplication or activating mutation in >70% of primary PAs, with KIAA1549:BRAF fusion genes being the most frequent genetic mechanism of BRAF activation. Approximately 90% of tumors show some form of MAPK activation as assessed by detection of ERK phosphorylation. Thus, alternative mechanisms of MAPK activation are yet to be discovered in 10-20% of cases. Here we describe an integrative approach combining genome-wide DNA methylation and mRNA expression analyses. In total, we studied 80 pilocytic astrocytomas, with a tissue microarray containing cores from 70 of these samples available for immunohistochemical validation. To identify novel subgroups and critical genes in PA pathogenesis, we performed methylation profiling and compared the resulting subgroups with transcriptome-based subgroups of overlapping tumors. Both experiments were performed on Illumina platforms, HumanWG-6 (expression profiling) and HumanMethylation27 BeadChip. Two CpG sites were analyzed for each of ∼14,000 promoters per sample. The 1000 most variant probes were selected for hierarchical consensus clustering for each platform. Identified molecular subgroups were investigated using Significance Analysis of Microarrays (SAM). Furthermore, to identify genes whose expression was potentially regulated by aberrant methylation, we performed an anti-correlation approach. By methylation profiling we could identify three subgroups in the 80 PA tumors that showed characteristic DNA methylation patterns. One subgroup that could also be derived by transcriptome analysis showed evidence of a CpG island methylator phenotype (PA-CIMP), since it displayed markedly elevated methylation of multiple genes compared with the other two groups. PA-CIMP tumors showed a lower frequency of MAPK alterations, including BRAF fusions or activating mutations, compared with the other subgroups. Patients with PA-CIMP tumors also showed an excellent prognosis, as none of these patients relapsed, despite 50% of the cases being non-cerebellar PAs. Thus, our PA-CIMP signature is potentially useful to identify tumors with a good prognosis, independent of location. This hypothesis is currently being validated in an independent series of 50 PAs. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4724. doi:10.1158/1538-7445.AM2011-4724