背景:神经母细胞瘤(NB)是一种复杂的疾病,目前对NB生物学的认识有限。基因组印迹的失调是恶性肿瘤中的常见事件。由于印迹基因在早期胎儿生长发育中起着至关重要的作用,提示其在NB发病机制中的作用。
方法:我们检查了369例NB肿瘤在49个印迹差异甲基化区(DMRs)的DNA甲基化模式的改变,并评估了其与总体生存概率以及肿瘤的选定临床和基因组特征的相关性。此外,进行了DNA甲基化和等位基因特异性拷贝数改变(CNAs)的综合分析,了解两个分子事件之间的相关性。
结果:确定了NB中具有异常甲基化模式的几个印迹区域。在>30%的NB样品中经历甲基化丢失的区域是与NDN基因注释的DMRs,SNRPN,IGF2,MAGEL2和HTR5A以及甲基化获得的区域为NNAT,RB1和GPR1。49个印迹DMRs中有6个的甲基化改变与总生存率降低有统计学意义:MIR886,RB1,NNAT/BLCAP,MAGEL2、MKRN3和INPP5F。RB1、NNAT/BLCAP和MKRN3进一步能够将低风险NB肿瘤(即缺乏MYCN扩增和11q缺失的肿瘤)分层为风险组。NNAT/BLCAP的甲基化改变,MAGEL2和MIR886独立于MYCN扩增或11q缺失和诊断年龄预测风险。对等位基因特异性CNA的研究表明,在NB肿瘤中显示大多数改变的印迹区域具有真实的表观遗传变化,而不是潜在CNA的结果。
结论:在NB肿瘤中经常发生印迹区域的异常甲基化,其中一些区域具有独立的预后价值。因此,这些指标可作为潜在的重要临床表观遗传标志物,用于确定预后不良的个体.将这些区域的甲基化状态与已建立的风险预测因子一起结合可以进一步改善NB患者的预后。
BACKGROUND: Neuroblastoma (NB) is a complex disease, and the current understanding of NB biology is limited. Deregulation in genomic imprinting is a common event in malignancy. Since imprinted genes play crucial roles in early fetal growth and development, their role in NB pathogenesis could be suggested.
METHODS: We examined alterations in DNA methylation patterns of 369 NB tumours at 49 imprinted differentially methylated regions (DMRs) and assessed its association with overall survival probabilities and selected clinical and genomic features of the tumours. In addition, an integrated analysis of DNA methylation and allele-specific copy number alterations (CNAs) was performed, to understand the correlation between the two molecular events.
RESULTS: Several imprinted regions with aberrant methylation patterns in NB were identified. Regions that underwent loss of methylation in > 30% of NB samples were DMRs annotated to the genes NDN, SNRPN, IGF2, MAGEL2 and HTR5A and regions with gain of methylation were NNAT, RB1 and GPR1. Methylation alterations at six of the 49 imprinted DMRs were statistically significantly associated with reduced overall survival: MIR886, RB1, NNAT/BLCAP, MAGEL2, MKRN3 and INPP5F. RB1, NNAT/BLCAP and MKRN3 were further able to stratify low-risk NB tumours i.e. tumours that lacked MYCN amplification and 11q deletion into risk groups. Methylation alterations at NNAT/BLCAP, MAGEL2 and MIR886 predicted risk independently of MYCN amplification or 11q deletion and age at diagnosis. Investigation of the allele-specific CNAs demonstrated that the imprinted regions that displayed most alterations in NB tumours harbor true epigenetic changes and are not result of the underlying CNAs.
CONCLUSIONS: Aberrant methylation in imprinted regions is frequently occurring in NB tumours and several of these regions have independent prognostic value. Thus, these could serve as potentially important clinical epigenetic markers to identify individuals with adverse prognosis. Incorporation of methylation status of these regions together with the established risk predictors may further refine the prognostication of NB patients.