Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma.
Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma.
复制标题
甲基-CPG结合结构域测序揭示了神经母细胞瘤中的预后甲基化特征。
DOI：
10.18632/oncotarget.6477
复制
发表时间：
2016-01-12
期刊：
影响因子：
--
通讯作者：
Vandesompele J
中科院分区：
文献类型：
--
作者：
Decock A;Ongenaert M;Cannoodt R;Verniers K;De Wilde B;Laureys G;Van Roy N;Berbegall AP;Bienertova-Vasku J;Bown N;Clément N;Combaret V;Haber M;Hoyoux C;Murray J;Noguera R;Pierron G;Schleiermacher G;Schulte JH;Stallings RL;Tweddle DA;Children’s Cancer and Leukaemia Group (CCLG);De Preter K;Speleman F;Vandesompele J
神经母细胞瘤预后预测的准确评估仍然具有挑战性。因此，本研究旨在建立新的预后肿瘤DNA甲基化生物标志物。总共分析了396例低风险和高风险原发性肿瘤，其中87例使用甲基-CpG结合结构域（MBD）测序进行分析，用于预后患者组之间的差异甲基化分析。随后，甲基化特异性PCR（MSP）检测开发了78个排名靠前的差异甲基化区域，并分别对132和177个样本的两个独立队列进行了测试。此外，使用新的统计框架来鉴定一组稳健的MSP测定，其甲基化评分（即甲基化测定的百分比）允许准确的结果预测。在个体目标水平上以及在组合的多标志物特征上进行生存分析。作为通过MBD测序进行差异DNA甲基化评估的结果，78个MSP测定中的58个被设计在神经母细胞瘤中先前未探索的区域中，并且36个位于非启动子或非编码区中。总共有5种MSP检测试剂（位于CCDC 177、NXPH 1、lnc-MRPL 3 -2、lnc-TREX 1 -1和一种位于8号染色体区域，无进一步注释）可预测无事件生存期，另外4种检测试剂（位于SPRED 3、TNFAIP 2、NPM 2和CYYR 1）也可预测总生存期。此外，建立了预测总体和无事件生存期的稳健的58标记甲基化特征。总之，这项研究包括迄今为止最大的神经母细胞瘤DNA甲基化生物标志物研究。我们鉴定并独立验证了几种新的预后生物标志物，以及一种预后性的58标记甲基化特征。
Accurate assessment of neuroblastoma outcome prediction remains challenging. Therefore, this study aims at establishing novel prognostic tumor DNA methylation biomarkers. In total, 396 low- and high-risk primary tumors were analyzed, of which 87 were profiled using methyl-CpG-binding domain (MBD) sequencing for differential methylation analysis between prognostic patient groups. Subsequently, methylation-specific PCR (MSP) assays were developed for 78 top-ranking differentially methylated regions and tested on two independent cohorts of 132 and 177 samples, respectively. Further, a new statistical framework was used to identify a robust set of MSP assays of which the methylation score (i.e. the percentage of methylated assays) allows accurate outcome prediction. Survival analyses were performed on the individual target level, as well as on the combined multimarker signature. As a result of the differential DNA methylation assessment by MBD sequencing, 58 of the 78 MSP assays were designed in regions previously unexplored in neuroblastoma, and 36 are located in non-promoter or non-coding regions. In total, 5 individual MSP assays (located in CCDC177, NXPH1, lnc-MRPL3-2, lnc-TREX1-1 and one on a region from chromosome 8 with no further annotation) predict event-free survival and 4 additional assays (located in SPRED3, TNFAIP2, NPM2 and CYYR1) also predict overall survival. Furthermore, a robust 58-marker methylation signature predicting overall and event-free survival was established. In conclusion, this study encompasses the largest DNA methylation biomarker study in neuroblastoma so far. We identified and independently validated several novel prognostic biomarkers, as well as a prognostic 58-marker methylation signature.