Stability of the CpG island methylator phenotype during glioma progression and identification of methylated loci in secondary glioblastomas

Abstract

BackgroundGrade IV glioblastomas exist in two forms, primary (de novo) glioblastomas (pGBM) that arise without precursor lesions, and the less common secondary glioblastomas (sGBM) which develop from earlier lower grade lesions. Genetic heterogeneity between pGBM and sGBM has been documented as have differences in the methylation of individual genes. A hypermethylator phenotype in grade IV GBMs is now well documented however there has been little comparison between global methylation profiles of pGBM and sGBM samples or of methylation profiles between paired early and late sGBM samples.MethodsWe performed genome-wide methylation profiling of 20 matched pairs of early and late gliomas using the Infinium HumanMethylation450 BeadChips to assess methylation at >485,000 cytosine positions within the human genome.ResultsClustering of our data demonstrated a frequent hypermethylator phenotype that associated with IDH1 mutation in sGBM tumors. In 80% of cases, the hypermethylator status was retained in both the early and late tumor of the same patient, indicating limited alterations to genome-wide methylation during progression and that the CIMP phenotype is an early event. Analysis of hypermethylated loci identified 218 genes frequently methylated across grade II, III and IV tumors indicating a possible role in sGBM tumorigenesis. Comparison of our sGBM data with TCGA pGBM data indicate that IDH1 mutated GBM samples have very similar hypermethylator phenotypes, however the methylation profiles of the majority of samples with WT IDH1 that do not demonstrate a hypermethylator phenotype cluster separately from sGBM samples, indicating underlying differences in methylation profiles. We also identified 180 genes that were methylated only in sGBM. Further analysis of these genes may lead to a better understanding of the pathology of sGBM vs pGBM.ConclusionThis is the first study to have documented genome-wide methylation changes within paired early/late astrocytic gliomas on such a large CpG probe set, revealing a number of genes that maybe relevant to secondary gliomagenesis.

DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors

“…Somatic mutations in IDH1 or IDH2 may be the first genetic driver in the development of many low-grade gliomas (Johnson et al, 2014; Lai et al, 2011; Watanabe et al, 2009). Genetic mutations in IDH genes induce a pattern of early epigenetic alterations known as the glioma CpG island methylator phenotype (G-CIMP) characterized by extensive remodeling of the DNA methylome (Hill et al, 2014; Noushmehr et al, 2010; Toyota et al, 1999; Turcan et al, 2012). The inactivation of other genes mutated in low-grade gliomas, such as ATRX (Jiao et al, 2012) and SMARCA4 (Johnson et al, 2014), is known to induce specific DNA methylation changes as well (Banine et al, 2005; Gibbons et al, 2000).…”

IDH1R132H decreases the proliferation of U87 glioma cells through upregulation of microRNA-128a

“…A number of molecular markers for GBM have been identified and are associated with diagnosis, prognosis and treatment. For example, somatic mutations in isocitrate dehydrogenase 1 ( IDH1 ) have been identified in GBM patients, particularly in secondary GBM, which evolves from lower-grade gliomas ( 2 ). In 90% of IDH1 mutations in gliomas, the arginine at position 132 is replaced by a histidine (R132H mutation) ( 3 ).…”

Differential gene methylation in paired glioblastomas suggests a role of immune response pathways in tumor progression

“…A recent study has reported that methylation levels are well preserved in lower-grade gliomas compared to secondary glioblastoma (70 % of them harboring IDH1 mutation) [10]. Accordingly, it is well established that IDH1/IDH2 mutations will induce a glioma CpG island hypermethylator phenotype (G-CIMP) and this phenotype is preserved throughout glioma progression [6,10].…”

“…In addition, promoter hypermethylation of methyl guanil methyltransferase gene (MGMT) is associated with an enhanced chemosensitivity [8,9]. Recent studies analyzing methylation levels at glioma progression have shown a strikingly stable methylation level when comparing initial lower-grade glioma with paired secondary GBM [10]. However, the analysis of methylation level at GBM progression in primary GBM is not well established and several studies analyzing methylation level at MGMT promoter are contradictory [6,[11][12][13].…”