CPI203, a BET inhibitor, down-regulates a consistent set of DNA synthesis genes across a wide array of glioblastoma lines [ATAC-seq]. CPI203, a BET inhibitor, down-regulates a consistent set of DNA synthesis genes across a wide array of glioblastoma lines [ATAC-seq]

Introduction: Glioblastomas utilize malignant gene expression pathways to drive growth. Many of these gene pathways are not directly accessible with molecularly targeted pharmacological agents. Chromatin-modifying compounds can alter gene expression and target glioblastoma growth pathways. In this study, we utilize a systematic screen of chromatin-modifying compounds on a panel of patient-derived glioblastoma lines to identify promising compounds and their associated gene targets. Methods: Five glioblastoma cell lines were subjected to a drug screen of 106 chromatin-modifying compounds representing 36 unique drug classes to determine the twelve most promising drug classes and the best candidate inhibitors in each class. These twelve drugs were then tested with a panel of twelve patient-derived gliomasphere lines to identify growth inhibition and corresponding gene expression patterns. Overlap analysis and weighted co-expression network analysis (WCGNA) were utilized to determine potential target genes and gene pathways. Results: The initial drug screen identified twelve candidate pharmacologic agents for further testing. Drug sensitivity testing indicated an overall high degree of variability between gliomasphere lines. However, CPI203 was the most consistently effective compound, and the BET inhibitor class was the most consistently effective class of compounds across the gliomasphere panel. Correspondingly, most of the compounds tested had highly variable effects on gene expression between gliomasphere lines. CPI203 stood out as the only compound to induce a consistent effect on gene expression across different gliomasphere lines, specifically down-regulation of DNA-synthesis genes. Amongst the twelve tested cell lines, high expression of CDKN2A and CDKN2B distinguished more drug sensitive from more drug resistant lines. WCGNA identified two oncogenic gene modules (FBXO5 and MELK) that were effectively downregulated by CPI203 (FBXO5) and ML228 (FBXO5 and MELK). Conclusions: The bromodomain inhibitor CPI203 induced relatively consistent effects on gene expression and growth across a variety of glioblastoma lines, specifically down-regulating genes associated with DNA replication. We propose that clinically effective BET inhibitors have the potential to induce consistent beneficial effects across a spectrum of glioblastomas. Overall design: 156 samples (12 cell lines × 12 drugs + controls), single condition per sample

研究背景：胶质母细胞瘤（Glioblastoma）通过恶性基因表达通路驱动肿瘤生长，其中多数通路无法通过分子靶向药物直接干预。染色质修饰类化合物可改变基因表达，靶向胶质母细胞瘤生长通路。本研究针对一组患者来源的胶质母细胞瘤细胞系，系统性筛选染色质修饰类化合物，以筛选出具有潜力的化合物及其相关基因靶点。
方法：选取5株胶质母细胞瘤细胞系，针对涵盖36个独特药物类别的106种染色质修饰类化合物开展药物筛选，以确定12个最具潜力的药物类别及每类中的最佳候选抑制剂。随后，将这12种药物在12株患者来源的神经球胶质瘤细胞系中进行测试，以评估其生长抑制效果及对应的基因表达谱。通过重叠分析及加权共表达网络分析（Weighted Correlation Network Analysis, WGCNA），确定潜在的靶基因及基因通路。
结果：初始药物筛选共鉴定出12种可供进一步测试的候选药理化合物。药物敏感性测试显示，不同神经球胶质瘤细胞系间的药物敏感性存在显著异质性。其中，CPI203是效果最为稳定的化合物，而BET抑制剂类（BET inhibitor）是本次神经球胶质瘤细胞系筛选中最稳定有效的药物类别。相应地，多数受试化合物对不同神经球胶质瘤细胞系的基因表达影响差异显著。CPI203是唯一能在不同神经球胶质瘤细胞系中诱导一致基因表达变化的化合物，其可特异性下调DNA合成相关基因。在12株受试细胞系中，CDKN2A与CDKN2B的高表达可区分药物敏感株与耐药株。WGCNA鉴定出两个致癌基因模块（FBXO5及MELK），其中CPI203可有效下调FBXO5，ML228则可同时下调FBXO5与MELK。
结论：溴结构域抑制剂CPI203可在多种胶质母细胞瘤细胞系中诱导相对一致的基因表达及生长抑制效果，特异性下调DNA复制相关基因。我们认为，临床有效的BET抑制剂有望在多种胶质母细胞瘤中产生稳定的获益效果。
整体实验设计：共包含156份样本（12株细胞系×12种药物+对照组），每份样本仅对应单一处理条件。