Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors. Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors

Atypical teratoid/rhabdoid tumors (AT/RTs) are pediatric brain tumors known for their aggressiveness, exceptionally low mutation rate, and aberrant but still unresolved epigenetic regulation. To evaluate methylation associated regulation in AT/RTs, we compared them to medulloblastomas and choroid plexus tumors by integrating DNA methylation (507 samples), gene expression (120 samples), and public transcription factor (TF) binding data. We showed that elevated DNA methylation masks the binding sites of TFs driving neural development and is associated with reduced transcription for specific neural regulators in AT/RTs. Hypermethylated sites largely behaved similarly in AT/RTs and pluripotent stem cells, revealing DNA methylation -driven halted cell differentiation. AT/RT-unique DNA hypermethylation was associated with polycomb repressive complex 2 members, like EZH2, and linked to suppressed genes with a role in neural development and tumorigenesis. The obtained results highlight and characterize these DNA methylation programs as drivers of AT/RT malignancy. Overall design: The cohort has material from 2 AT/RT patients, 3 MB patients and 5 Coroid plexus tumor (PLEX) patients. It consists of 10 RNA-seq samples and 10 RRBS samples from the same tumours, but due to ethical reasons, the raw material cannot be published. Processed files (Gene counts and the methylation percentages in regional level (1000bp regions) are provided. Additionally, CUT&RUN data from 4 cell lines (3 AT/RT, 1 MB) with two technical replicates each. The processed MACS3 peaks are provided. CUT&RUN sequencing for NEUROD1 for 3 AT/RT cell lines as well as 1 MB cell lines. ***The submitter declares that Raw data cannot be published due to ethical reasons***

非典型畸胎瘤/横纹肌样瘤（Atypical teratoid/rhabdoid tumors, AT/RTs）是一类恶性程度极高的儿童脑肿瘤，以突变率极低、表观遗传调控异常且具体机制尚未阐明为特征。为探究AT/RTs中与甲基化相关的调控机制，我们将其与髓母细胞瘤及脉络丛肿瘤进行比对，整合了DNA甲基化数据（共507例样本）、基因表达数据（共120例样本）以及公开的转录因子（transcription factor, TF）结合数据集。本研究证实，升高的DNA甲基化会掩盖驱动神经发育的转录因子结合位点，并与AT/RTs中特定神经调控因子的转录水平下调相关。高甲基化位点在AT/RTs与多能干细胞中表现出高度相似的特征，揭示了DNA甲基化介导的细胞分化阻滞现象。AT/RT特异性的DNA高甲基化与多梳抑制复合体2（polycomb repressive complex 2）成员（如EZH2）存在关联，并与参与神经发育及肿瘤发生的表达抑制基因相关。本研究结果明确了此类DNA甲基化程序作为AT/RT恶性表型驱动因素的作用，并对其进行了系统表征。

总体设计：本队列包含2例AT/RT患者、3例髓母细胞瘤患者及5例脉络丛肿瘤（PLEX）患者的样本。同一肿瘤样本分别制备了10份RNA测序（RNA-seq）样本与10份RRBS测序样本，但受伦理限制，原始数据无法公开。本研究提供了处理后的数据集：包括基因计数数据以及1000bp区域水平的甲基化百分比数据。此外，本研究还提供了4种细胞系的CUT&RUN数据：包含3株AT/RT细胞系与1株髓母细胞瘤细胞系，每种细胞系设置2次技术重复，处理后的MACS3峰文件已同步提供。其中还包含针对3株AT/RT细胞系及1株髓母细胞瘤细胞系的NEUROD1蛋白CUT&RUN测序数据。

***提交者声明：受伦理因素限制，原始数据无法公开***