ZFHX4 and CHD4 ChIP sequencing in glioblastoma tumor initiating cells

Glioblastomas (GBM) harbor subpopulations of therapy-resistant tumor initiating cells (TICs) that are self-renewing and multipotent. To understand the regulation of the TIC state, we performed an image-based screen for genes regulating GBM TIC maintenance and identified ZFHX4, a 397-kDa transcription factor. ZFHX4 is required to maintain TIC-associated phenotypes in vitro, suggesting that ZFHX4 regulates TIC differentiation, and its suppression increases glioma-free survival in intracranial xenografts. ZFHX4 interacts with CHD4, a core member of the NuRD (nucleosome remodeling and deacetylase) complex. ZFHX4 and CHD4 bind to overlapping sets of genomic loci and control similar gene expression programs. Using expression data derived from GBM patients, we demonstrate ZFHX4 is a master regulator of CHD4-mediated gene expression. These observations define ZFHX4 as a regulatory factor that links the chromatin remodeling NuRD complex and the GBM TIC state. Overall design: Examination of binding of ZFHX4 and CHD4 across the human genome, using the 0308 tumor initiating cell line. Two replicates for each protein, compared to whole cell extract inputs.

胶质母细胞瘤（Glioblastomas, GBM）携带有治疗抗性的肿瘤起始细胞（Tumor Initiating Cells, TICs）亚群，这类细胞具备自我更新能力且具有多向分化潜能。为阐明TIC状态的调控机制，本研究开展了基于成像的筛选实验，以寻找调控GBM TIC维持的基因，并鉴定出ZFHX4——一种分子量为397 kDa的转录因子。ZFHX4是体外维持TIC相关表型所必需的，这提示ZFHX4可调控TIC的分化，而抑制ZFHX4能够延长颅内异种移植模型中的无胶质瘤生存期。ZFHX4可与CHD4相互作用，而CHD4是NuRD（核小体重塑与去乙酰化酶）复合物的核心组分。ZFHX4与CHD4可结合至重叠的基因组位点，并调控相似的基因表达程序。通过使用GBM患者来源的表达谱数据，本研究证实ZFHX4是CHD4介导的基因表达过程的核心调控因子。上述研究结果将ZFHX4定义为一类连接染色质重塑NuRD复合物与GBM TIC状态的调控因子。实验总体设计：以0308肿瘤起始细胞系为研究对象，检测ZFHX4与CHD4在人类全基因组范围内的结合情况；每个蛋白设置两个生物学重复，并以全细胞提取物作为输入对照样本。