Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - tumour ChIPseq data. Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - tumour ChIPseq data

Glioblastomas in adult patients are classified into four subtypes, IDH, MES, RTK I, and RTK II, based on DNA-methylation and RNA-expression data. Tumour subtype transitions are common during treatment, and transitions to the mesenchymal (MES) subtype are associated with therapy resistance and adverse prognosis. Here, we present DNA methylome and histone modification data of glioblastoma primary tumours and find that glioblastoma subtypes differ in their enhancer landscapes. Using Core Regulatory Circuitry analysis of chromatin and orthogonal analysis of RNA-derived gene regulatory networks, we identified 38 subtype Master Regulators whose cell population-specific activities we further mapped in single-cell RNA sequencing data. These analyses identified the oligodendrocyte precursor marker and chromatin modifier SRY-Box 10 (SOX10) as a master regulator in RTK I tumours. In vitro functional studies demonstrated that SOX10 loss causes a subtype switch analogous to the proneural-mesenchymal Transition observed in patients at the transcriptomic, epigenetic and phenotypic levels. This subtype transition is dependent on the activity of the SOX10 and enhancer co-factor Bromodomain Containing 4 (BRD4). Sox10 repression in an in vivo syngeneic graft glioblastoma mouse model results in increased tumour invasion, immune cell infiltration and significantly reduced survival, reminiscent of progressive human glioblastoma. These results identify SOX10 as a bona fide master regulator of the RTK I subtype, with both tumour cell-intrinsic and microenvironmental effects, highlighting that both glioblastoma cell plasticity and their tumour-microenvironment interactions are important contributors to tumour phenotypes. Overall design: 20 GBs (IDH: 6; MES: 4; RTK I and RTK II: 5 each) were characterised by histone mark ChIPseq (H3K27ac, H3K27me3, H3K4me1, H3K4me3, H3K36me3, H3K9me3, with WGS as input control). The following analyses were performed on the above data: - ChromHMM analysis (using the Roadmap Epigenome 18-state model) - superenhancer analysis (on H3K27ac data) - active enhancer analysis (combining H3K27ac, H3K4me1 data) Please note that [1] the processed data files generated from multiple samples are linked as Series supplementary files and are indicated in the corresponding sample description field [2] Raw data requires controlled access and is deposited at EGAS00001003230.

成人胶质母细胞瘤（Glioblastomas）依据DNA甲基化与RNA表达数据，可分为IDH、MES、RTK I及RTK II四种亚型。治疗过程中肿瘤亚型转换现象较为常见，其中向间质型（MES）亚型的转换与治疗耐药及不良预后密切相关。

本研究公开了胶质母细胞瘤原发肿瘤的DNA甲基化组学与组蛋白修饰组学数据，并发现胶质母细胞瘤各亚型的增强子景观存在显著差异。通过对染色质开展核心调控回路（Core Regulatory Circuitry）分析，以及对RNA来源的基因调控网络进行正交验证分析，我们共鉴定出38个亚型特异性主调控因子，并进一步通过单细胞RNA测序数据绘制了这些因子在不同细胞群中的活性分布。

上述分析将少突胶质细胞前体细胞标志物兼染色质修饰因子SRY盒转录因子10（SOX10）鉴定为RTK I亚型的核心主调控因子。体外功能实验证实，敲低SOX10可引发类似患者中所见的原神经-间质转化，且该亚型转换在转录组、表观基因组及表型层面均有体现。

该亚型转换依赖于SOX10与增强子辅因子含溴结构域蛋白4（BRD4）的协同活性。在体内同源移植胶质母细胞瘤小鼠模型中敲低Sox10，可导致肿瘤侵袭性增强、免疫细胞浸润增加，并显著缩短小鼠生存期，这一表型与人类进展期胶质母细胞瘤的特征相符。

上述研究结果证实SOX10是RTK I亚型的真实核心主调控因子，同时兼具肿瘤细胞内在调控与肿瘤微环境调控双重作用，这提示胶质母细胞瘤的细胞可塑性及其与肿瘤微环境的相互作用，均是影响肿瘤表型的重要因素。

整体实验设计：本研究对20例胶质母细胞瘤样本（IDH型6例、MES型4例、RTK I型与RTK II型各5例）进行了组蛋白标记染色质免疫沉淀测序（ChIPseq），检测的组蛋白修饰包括H3K27ac、H3K27me3、H3K4me1、H3K4me3、H3K36me3、H3K9me3，并以全基因组测序（WGS）作为输入对照。

基于上述数据，我们开展了以下分析：
- ChromHMM分析（采用Roadmap表观基因组18状态模型）
- 超级增强子分析（基于H3K27ac数据）
- 活性增强子分析（整合H3K27ac与H3K4me1数据）

请注意：
[1] 多样本生成的已处理数据文件以系列补充文件形式关联，并在对应样本描述字段中注明；
[2] 原始数据需受控访问，已存储于EGAS00001003230。