Department of Neurology, David Geffen School of Medicine at the University of California Los Angeles, 90095, USA.
J Natl Cancer Inst. 2012 Oct 3;104(19):1458-69. doi: 10.1093/jnci/djs357. Epub 2012 Sep 3.
Mutations in isocitrate dehydrogenase 1 (IDH1) and associated CpG island hypermethylation represent early events in the development of low-grade gliomas and secondary glioblastomas. To identify candidate tumor suppressor genes whose promoter methylation may contribute to gliomagenesis, we compared methylation profiles of IDH1 mutant (MUT) and IDH1 wild-type (WT) tumors using massively parallel reduced representation bisulfite sequencing.
Reduced representation bisulfite sequencing was performed on ten pathologically matched WT and MUT glioma samples and compared with data from a methylation-sensitive restriction enzyme technique and data from The Cancer Genome Atlas (TCGA). Methylation in the gene retinol-binding protein 1 (RBP1) was identified in IDH1 mutant tumors and further analyzed with primer-based bisulfite sequencing. Correlation between IDH1/IDH2 mutation status and RBP1 methylation was evaluated with Spearman correlation. Survival data were collected retrospectively and analyzed with Kaplan-Meier and Cox proportional hazards analysis. All statistical tests were two-sided.
Methylome analysis identified coordinated CpG island hypermethylation in IDH1 MUT gliomas, consistent with previous reports. RBP1, important in retinoic acid metabolism, was found to be hypermethylated in 76 of 79 IDH1 MUT, 3 of 3 IDH2 MUT, and 0 of 116 IDH1/IDH2 WT tumors. IDH1/IDH2 mutation was highly correlated with RBP1 hypermethylation (n = 198; Spearman R = 0.94, 95% confidence interval = 0.92 to 0.95, P < .001). The Cancer Genome Atlas showed IDH1 MUT tumors (n = 23) to be RBP1-hypermethylated with decreased RBP1 expression compared with WT tumors (n = 124). Among patients with primary glioblastoma, patients with RBP1-unmethylated tumors (n = 102) had decreased median overall survival compared with patients with RBP1-methylated tumors (n = 22) (20.3 months vs 36.8 months, respectively; hazard ratio of death = 2.48, 95% confidence interval = 1.30 to 4.75, P = .006).
RBP1 promoter hypermethylation is found in nearly all IDH1 and IDH2 mutant gliomas and is associated with improved patient survival. Because RBP1 is involved in retinoic acid synthesis, our results suggest that dysregulation of retinoic acid metabolism may contribute to glioma formation along the IDH1/IDH2-mutant pathway.
异柠檬酸脱氢酶 1（IDH1）突变和相关的 CpG 岛甲基化是低级别胶质瘤和继发性胶质母细胞瘤发生的早期事件。为了鉴定可能导致胶质瘤发生的候选肿瘤抑制基因，我们使用大规模平行简化代表性亚硫酸氢盐测序比较了 IDH1 突变（MUT）和 IDH1 野生型（WT）肿瘤的甲基化谱。
对十个病理匹配的 WT 和 MUT 胶质瘤样本进行简化代表性亚硫酸氢盐测序，并与甲基敏感限制性内切酶技术和癌症基因组图谱（TCGA）的数据进行比较。在 IDH1 突变肿瘤中发现视黄醇结合蛋白 1（RBP1）的基因启动子甲基化，并进一步使用基于引物的亚硫酸氢盐测序进行分析。用 Spearman 相关评估 IDH1/IDH2 突变状态与 RBP1 甲基化之间的相关性。收集回顾性生存数据并进行 Kaplan-Meier 和 Cox 比例风险分析。所有统计检验均为双侧。
甲基化组分析确定 IDH1 MUT 胶质瘤中存在协同的 CpG 岛过度甲基化，与先前的报道一致。视黄酸代谢中重要的 RBP1 被发现 79 例 IDH1 MUT、3 例 IDH2 MUT 和 116 例 IDH1/IDH2 WT 肿瘤中有 76 例过度甲基化。IDH1/IDH2 突变与 RBP1 过度甲基化高度相关（n = 198；Spearman R = 0.94，95%置信区间 = 0.92 至 0.95，P <.001）。癌症基因组图谱显示 IDH1 MUT 肿瘤（n = 23）与 WT 肿瘤（n = 124）相比 RBP1 过度甲基化，RBP1 表达降低。在原发性胶质母细胞瘤患者中，RBP1 未甲基化肿瘤（n = 102）的中位总生存期短于 RBP1 甲基化肿瘤（n = 22）（分别为 20.3 个月和 36.8 个月；死亡风险比为 2.48，95%置信区间为 1.30 至 4.75，P =.006）。
几乎所有 IDH1 和 IDH2 突变的胶质瘤都发现 RBP1 启动子过度甲基化，与患者生存改善相关。因为 RBP1 参与视黄酸的合成，我们的结果表明视黄酸代谢的失调可能沿着 IDH1/IDH2 突变途径导致胶质瘤的形成。
