Division of Genetics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas;
J Neurosurg. 2013 Oct;119(4):899-906. doi: 10.3171/2013.7.JNS13311. Epub 2013 Aug 9.
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.
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.
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).
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.
尽管大多数脑膜瘤为良性，但约 20%为非典型（Ⅱ级或Ⅲ级），其死亡率和发病率更高。识别具有更大恶性潜能的肿瘤具有重要的临床价值。本项经验证的全基因组甲基化研究旨在比较Ⅰ级与Ⅱ级和Ⅲ级脑膜瘤，以发现非典型脑膜瘤中异常甲基化的基因。
在俄亥俄州脑肿瘤研究中发现新诊断的脑膜瘤患者。使用 Infinium HumanMethylation27 BeadChip（Illumina，Inc.）对每个样本的 14000 个基因中的 27578 个 CpG 位点进行检测，共检测 33 个样本（3 个非典型）。为了验证结果，使用 Infinium HumanMethylation450 BeadChip（Illumina，Inc.）对基因组中 450000 个 CpG 位点的胞嘧啶进行检测，验证集包含 7 个重复（3 个非典型）和 12 个独立样本（6 个非典型）。对两组良性和非典型脑膜瘤之间的甲基化差异采用非参数 Wilcoxon 精确检验进行检验。为每组生成热图。对一组 20 个（10 个非典型）样本（包括 11 个重复）进行 Western blot 分析，验证了甲基化强度差异最大的 2 个探针的甲基化结果。
发现数组在良性和非典型脑膜瘤之间识别出 95 个具有差异甲基化的探针，在热图上进行视觉检查时创建了 2 个可区分的组，对应于肿瘤分级。验证数组评估了 87 个不同的探针，显示有 9 个探针存在甲基化差异。在热图检查中，该数组的结果还表明存在 2 个与组织学分级对应的主要组。IGF2BP1 和 PDCD1 是两种可以增加肿瘤恶性潜能的蛋白质，是强度差异最大的 2 个探针，这两种探针的非典型脑膜瘤的蛋白质产量中位数均降低，尽管这在统计学上并不显著（IGF2BP1 的 p = 0.970，PDCD1 的 p = 1）。
对良性和非典型脑膜瘤进行全基因组甲基化分析，确定了 9 个可靠的差异甲基化基因，其中 IGF2BP1 和 PDCD1 的差异最大。这些位点甲基化增加与侵袭性表型相关的机制尚不清楚。未来的研究可能会研究这种机制，以及 IGF2BP1 作为其他看似良性脑膜瘤中致病性的标志物的效用。
