Abstract：
Gene co-expression networks may encode hitherto inadequately recognized vulnerabilities for adult gliomas. By identifying evolutionally conserved gene co-expression modules around EGFR (EM) or PDGFRA (PM), we recently proposed an EM/PM classification scheme, which assigns IDH-wildtype glioblastomas (GBM) into the EM subtype committed in neural stem cell compartment, IDH-mutant astrocytomas and oligodendrogliomas into the PM subtype committed in early oligodendrocyte lineage. Here, we report the identification of EM/PM subtype-specific gene co-expression networks and the characterization of hub gene polypyrimidine tract-binding protein 1 (PTBP1) as a genomic alteration-independent vulnerability in IDH-wildtype GBM. Supervised by the EM/PM classification scheme, we applied weighted gene co-expression network analysis to identify subtype-specific global gene co-expression modules. These gene co-expression modules were characterized for their clinical relevance, cellular origin and conserved expression pattern during brain development. Using lentiviral vector-mediated constitutive or inducible knockdown, we characterized the effects of PTBP1 on the survival of IDH-wildtype GBM cells, which was complemented with the analysis of PTBP1-depedent splicing pattern and overexpression of splicing target neuron-specific CDC42 (CDC42-N) isoform. Transcriptomes of adult gliomas can be robustly assigned into 4 large gene co-expression modules that are prognostically relevant and are derived from either malignant cells of the EM/PM subtypes or tumor microenvironment. The EM subtype is associated with a malignant cell-intrinsic gene module involved in pre-mRNA splicing, DNA replication and damage response, and chromosome segregation, and a microenvironment-derived gene module predominantly involved in extracellular matrix organization and infiltrating immune cells. The PM subtype is associated with two malignant cell-intrinsic gene modules predominantly involved in transcriptional regulation and mRNA translation, respectively. Expression levels of these gene modules are independent prognostic factors and malignant cell-intrinsic gene modules are conserved during brain development. Focusing on the EM subtype, we identified PTBP1 as the most significant hub for the malignant cell-intrinsic gene module. PTBP1 is not altered in most glioma genomes. PTBP1 represses the conserved splicing of CDC42-N. PTBP1 knockdown or CDC42-N overexpression disrupts actin cytoskeleton dynamics, causing accumulation of reactive oxygen species and cell apoptosis. PTBP1-mediated repression of CDC42-N splicing represents a potential genomic alteration-independent, developmentally conserved vulnerability in IDH-wildtype GBM.
摘要：
基因共表达网络可能编码迄今为止尚未充分认识到的成人神经胶质瘤的脆弱性。通过确定EGFR（EM）或PDGFRA（PM）周围的进化保守基因共表达模块，我们最近提出了EM/PM分类方案，将IDH-野生型胶质母细胞瘤（GBM）分配到神经干细胞区室中的EM亚型中，IDH突变型星形细胞瘤和少突胶质细胞瘤进入PM亚型的早期少突胶质细胞谱系。这里,我们报道了EM/PM亚型特异性基因共表达网络的鉴定以及hub基因多嘧啶束结合蛋白1(PTBP1)作为IDH野生型GBM中不依赖基因组改变的易损性的特征.由EM/PM分类方案监督，我们应用加权基因共表达网络分析来鉴定亚型特异性全局基因共表达模块.这些基因共表达模块的特征在于它们的临床相关性，脑发育过程中的细胞起源和保守表达模式。使用慢病毒载体介导的组成型或诱导型敲除，我们表征了PTBP1对IDH野生型GBM细胞存活的影响，PTBP1抑制剪接模式的分析和剪接靶神经元特异性CDC42（CDC42-N）同工型的过表达。成人神经胶质瘤的转录组可以被稳健地分配到4个大的基因共表达模块中，这些模块在预后上是相关的，并且源自EM/PM亚型的恶性细胞或肿瘤微环境。EM亚型与参与前mRNA剪接的恶性细胞固有基因模块相关，DNA复制和损伤反应，和染色体分离，以及主要参与细胞外基质组织和浸润免疫细胞的微环境衍生基因模块。PM亚型与两个主要参与转录调控和mRNA翻译的恶性细胞固有基因模块相关。分别。这些基因模块的表达水平是独立的预后因素，恶性细胞固有基因模块在脑发育过程中是保守的。专注于EM子类型，我们确定PTBP1是恶性细胞固有基因模块最重要的中心.PTBP1在大多数神经胶质瘤基因组中没有改变。PTBP1抑制CDC42-N的保守剪接。PTBP1敲低或CDC42-N过表达破坏肌动蛋白细胞骨架动力学，引起活性氧积累和细胞凋亡。PTBP1介导的CDC42-N剪接的抑制代表了一个潜在的基因组改变无关，IDH野生型GBM中发育保守的脆弱性。
