Methylation markers of malignant potential in meningiomas

Abstract

Object Although most meningiomas are benign, about 20% are atypical (Grade II or III) and have increased mortality and morbidity. Identifying tumors with greater malignant potential can have significant clinical value. This validated genome-wide methylation study comparing Grade I with Grade II and III meningiomas aims to discover genes that are aberrantly methylated in atypical meningiomas. Methods Patients with newly diagnosed meningioma were identified as part of the Ohio Brain Tumor Study. The Infinium HumanMethylation27 BeadChip (Illumina, Inc.) was used to interrogate 27,578 CpG sites in 14,000 genes per sample for a discovery set of 33 samples (3 atypical). To verify the results, the Infinium HumanMethylation450 BeadChip (Illumina, Inc.) was used to interrogate 450,000 cytosines at CpG loci throughout the genome for a verification set containing 7 replicates (3 atypical), as well as 12 independent samples (6 atypical). A nonparametric Wilcoxon exact test was used to test for difference in methylation between benign and atypical meningiomas in both sets. Heat maps were generated for each set. Methylation results were validated for the 2 probes with the largest difference in methylation intensity by performing Western blot analysis on a set of 20 (10 atypical) samples, including 11 replicates. Results The discovery array identified 95 probes with differential methylation between benign and atypical meningiomas, creating 2 distinguishable groups corresponding to tumor grade when visually examined on a heat map. The validation array evaluated 87 different probes and showed that 9 probes were differentially methylated. On heat map examination the results of this array also suggested the existence of 2 major groups that corresponded to histological grade. IGF2BP1 and PDCD1, 2 proteins that can increase the malignant potential of tumors, were the 2 probes with the largest difference in intensity, and for both of these the atypical meningiomas had a decreased median production of protein, though this was not statistically significant (p = 0.970 for IGF2BP1 and p = 1 for PDCD1). Conclusions A genome-wide methylation analysis of benign and atypical meningiomas identified 9 genes that were reliably differentially methylated, with the strongest difference in IGF2BP1 and PDCD1. The mechanism why increased methylation of these sites is associated with an aggressive phenotype is not evident. Future research may investigate this mechanism, as well as the utility of IGF2BP1 as a marker for pathogenicity in otherwise benign-appearing meningiomas.

Global epigenetic profiling identifies methylation subgroups associated with recurrence-free survival in meningioma

“…They profiled 19 WHO grade I, II and III meningiomas and similar with Vengoechea et al [74], Gao’s group looked for differences in methylation between benign and malignant meningioma groups. They concluded that WHO grade II and III meningiomas were globally hypomethylated compared to WHO grade I tumors but they did not offer much details and probe identification except for 15 hypomethylated genes that were further investigated for expression analysis.…”

“…With time, molecular advances allowed interrogation at a larger number of CpG loci [35] culminating with the methylation assays from Illumina (27k and 450k) interrogating approximately 27.000 and 450.000 CpG loci [74,21]. To the best of our knowledge only three studies addressed global methylation in meningiomas [35,74,21].…”

“…With time, molecular advances allowed interrogation at a larger number of CpG loci [35] culminating with the methylation assays from Illumina (27k and 450k) interrogating approximately 27.000 and 450.000 CpG loci [74,21]. To the best of our knowledge only three studies addressed global methylation in meningiomas [35,74,21]. Kishida et al in the first global methylation meningioma study [35] interrogated 30 WHO grade I and II meningiomas using methylated CpG island amplification microarrays for 6157 genes and identified 198 significantly different genes among 3 clusters obtained by unsupervised hierarchical clustering and consensus clustering analysis.…”

“…However, little is known about global methylation profiles of meningioma [21,35,74], and their clinical implications are not yet well understood. Moreover, a deeper understanding of methylation in meningioma may increase our understanding regarding meningioma tumorigenesis.…”

Atypical and anaplastic meningioma: outcomes in a population based study

“…In one study, authors explored the expression of pro-apoptotic and anti-apoptotic factors in 67 AAM patients, they found that low expression of CASP3 and BAX, and overexpression of survivin and MDM2 were associated with recurrence [33]. Additionally, methylation of PDCD1 and IGF2BP1 was found to correlate with increased malignant potential and associated with an aggressive phenotype [34]. Other cytogenetic alterations and specific gene mutations have been identified in patients with AAM that differ from those found in WHO grade I meningiomas [35].…”