背景:脑肿瘤分子亚群的准确鉴定越来越重要。我们旨在建立最准确和可重复的室管膜瘤亚组生物标志物检测技术,来自国际小儿肿瘤学会(SIOP)的147例室管膜瘤II试验参与者,参加泛欧洲“儿童和青少年室管膜瘤生物标志物(BIOMECA)”研究。
方法:在六个欧洲BIOMECA实验室中,我们评估了表观遗传谱分析(DNA甲基化阵列);核p65-RELA的免疫组织化学(IHC),H3K27me3和Tenascin-C;通过FISH和MLPA进行拷贝数分析(1q,CDKN2A),和MIP和DNA甲基化阵列(全基因组拷贝数评估);通过RT-PCR和测序分析ZFTA和YAP1融合体,纳米弦和分裂的FISH。
结果:DNA甲基化分析将65.3%(n=96/147)的病例分类为EPN-PFA,将15%(n=22/147)的病例分类为ST-ZFTA融合阳性。H3K27me3的免疫组织化学损失是EPN-PFA的可重复且准确的替代标记(三个中心的敏感性为99-100%)。P65-RELA的IHC,FISH,和基于RNA的分析有效地鉴定了ZFTA-和YAP1-融合的幕上室管膜瘤。使用FISH检测1q增益仅表现出57%的中心间一致性和低灵敏度和特异性,而MIP,MLPA和基于DNA甲基化的方法显示出更高的准确性。
结论:我们确认,在前瞻性试验队列中,H3K27me3免疫组织化学是一个强大的EPN-PFA生物标志物。应放弃Tenascin-C作为PFA标记。DNA甲基化和MIP阵列是1q增益拷贝数分析的有效工具,6q和CDKN2A损失,而FISH不足。融合检测成功,但是罕见的新型融合需要更广泛的技术。最后,我们提出测试集来指导未来的诊断方法。
Accurate identification of brain tumor molecular subgroups is increasingly important. We aimed to establish the most accurate and reproducible ependymoma subgroup biomarker detection techniques, across 147 cases from International Society of Pediatric Oncology (SIOP) Ependymoma II
trial participants, enrolled in the pan-European \"Biomarkers of Ependymoma in Children and Adolescents (BIOMECA)\"
study.
Across 6 European BIOMECA laboratories, we evaluated epigenetic profiling (DNA methylation array); immunohistochemistry (IHC) for nuclear p65-RELA, H3K27me3, and
Tenascin-C; copy number analysis via fluorescent in situ hybridization (FISH) and MLPA (1q, CDKN2A), and MIP and DNA methylation array (genome-wide copy number evaluation); analysis of ZFTA- and YAP1-fusions by RT-PCR and sequencing, Nanostring and break-apart FISH.
DNA Methylation profiling classified 65.3% (n = 96/147) of cases as EPN-PFA and 15% (n = 22/147) as ST-ZFTA fusion-positive. Immunohistochemical loss of H3K27me3 was a reproducible and accurate surrogate marker for EPN-PFA (sensitivity 99%-100% across 3 centers). IHC for p65-RELA, FISH, and RNA-based analyses effectively identified ZFTA- and YAP-fused supratentorial ependymomas. Detection of 1q gain using FISH exhibited only 57% inter-center concordance and low sensitivity and specificity while MIP, MLPA, and DNA methylation-based approaches demonstrated greater accuracy.
We confirm, in a prospective
trial cohort, that H3K27me3 immunohistochemistry is a robust EPN-PFA biomarker.
Tenascin-C should be abandoned as a PFA marker. DNA methylation and MIP arrays are effective tools for copy number analysis of 1q gain, 6q, and CDKN2A loss while FISH is inadequate. Fusion detection was successful, but rare novel fusions need more extensive technologies. Finally, we propose test sets to guide future diagnostic approaches.