Integrative analysis of exome-seq, RNA-seq, ATAC-seq (bulk and single-cell), and Hi-C data generated from 3-D spatially mapped samples acquired during surgical resection from 10 patients diagnosed with IDH-WT glioblastoma

Glioblastoma (GBM), the most common primary brain cancer in adults, remains incurable with no targeted therapies approved despite decades of investigation into its molecular landscape. Treatment failure is attributed to intratumoral heterogeneity in the GBM genome and epigenome, which foster tumor evolution and selection of resistant clones. However, tumor evolution and intratumoral heterogeneity remain poorly understood on the level of the whole tumor as most studies are based on single samples per patient and lack spatial context. Here, we have used 3-D neuronavigation during surgical resection for 10 primary IDH-WT GBM patients to collect 102 samples representing maximal tumor diversity, each mapped by 3-D spatial coordinates. We have applied a strategic set of genomic and epigenomic assays spanning multiple levels of resolution to discover, orthogonally validate, and functionally assess drivers of tumor evolution and intratumoral heterogeneity. These include extrachromosomal DNA amplifications, chromothripsis events, inversions, and translocations that disrupt both the GBM genome and epigenome while generating fusion transcripts and opportunities for therapeutic intervention. We define epigenomic programs that contribute to GBM evolution and intratumoral heterogeneity, revealing their 3-D spatial patterning within whole tumors and their cell type(s) of origin in single-cell data from the same tumor samples. Notably, we distinguish neuronal, glial, and immune programs aberrantly active in tumor cells from their counterparts in normal cells and discover NEUROD1, JUN/FOS, and NF1 transcription factors as key drivers of GBM evolution and growth. Collectively, these data provide unprecedented insight into GBM evolution and intratumoral heterogeneity from single-cell to whole-tumor resolution, redefining current understanding and providing a rich resource of targets for therapeutic investigation.EGA study EGAS00001006785

胶质母细胞瘤（Glioblastoma, GBM）是成人最常见的原发性脑恶性肿瘤，尽管数十年来对其分子图谱开展了深入研究，目前仍无获批的靶向治疗方案，且始终无法治愈。治疗失败的根源在于GBM基因组与表观基因组层面的肿瘤内异质性，该异质性可促进肿瘤演化并筛选出耐药克隆。然而，由于多数研究仅纳入每位患者的单一样本且缺乏空间维度信息，人们对整体肿瘤层面的肿瘤演化与肿瘤内异质性仍知之甚少。本研究针对10例IDH野生型原发性GBM患者，在手术切除过程中采用三维神经导航技术采集了102份样本以最大化覆盖肿瘤异质性，所有样本均标注了三维空间坐标。研究团队采用覆盖多分辨率层级的基因组与表观基因组检测策略，对肿瘤演化与肿瘤内异质性的驱动因素进行发掘、正交验证与功能评估，其中包括破坏GBM基因组与表观基因组、同时产生融合转录本并为治疗干预提供靶点的染色体外DNA扩增、染色体碎裂、倒位与易位事件。本研究明确了参与GBM演化与肿瘤内异质性的表观基因组程序，揭示了这些程序在整体肿瘤内的三维空间分布模式，以及其在同肿瘤样本单细胞数据中的细胞起源类型。值得注意的是，我们将肿瘤细胞中异常激活的神经元、胶质细胞与免疫相关程序与正常细胞中的对应程序加以区分，并发现NEUROD1、JUN/FOS与NF1转录因子是GBM演化与增殖的关键驱动因素。综上，本研究从单细胞到整体肿瘤分辨率层面，为解析GBM演化与肿瘤内异质性提供了前所未有的视角，重塑了学界对该疾病的现有认知，并为治疗靶点研究提供了丰富的资源。本数据集对应的EGA研究编号为EGAS00001006785。