ZFHX4 Interacts with the NuRD Core Member CHD4 and Regulates the Glioblastoma Tumor-Initiating Cell State

Abstract

Summary 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 and normal human neural precursor cell phenotypes in vitro, suggesting that ZFHX4 regulates 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 found that ZFHX4 significantly affects CHD4-mediated gene expression perturbations, which defines ZFHX4 as a master regulator of CHD4. These observations define ZFHX4 as a regulatory factor that links the chromatin remodeling NuRD complex and the GBM TIC state.

Cancer stem cells in glioblastoma

“…CSC regulation converges on MYC, which occurs in the presence of MYC-mediated cancer cell survival and proliferation programs Zheng et al 2008;Wurdak et al 2010;Chan et al 2012;Fang et al 2014). Additional transcription factors have been identified as important for CSC identity, including STAT3 (Sherry et al 2009), SOX2 (Gangemi et al 2009), FOXM1 (Joshi et al 2013), FOXG1 (Verginelli et al 2013), GLI1 (Clement et al 2007), ASCL1 (Rheinbay et al 2013), ZFX , NANOG (Zbinden et al 2010), and ZFHX4 (Chudnovsky et al 2014), which recruit necessary chromatin remodeling factors to promote maintenance of the glioma CSC state. By using epigenome-wide mapping of cellular chromatin state, Suva et al (2014) identified a core set of four transcription factors in proneural GBM able to reprogram differentiated tumor cells into glioma CSCs.…”

A Systems Approach to Drug Discovery in Alzheimer's Disease

“…The corresponding human PC interactome was produced by ARACNe analysis of a set of gene expression profiles from~200 patient-derived PC samples, representing the full spectrum of disease progression. Comparison of the human and murine interactomes, using a novel algorithm, revealed that 70% of the regulatory programs in PC are highly conserved between these 2 species, including those of 2 synergistic master regulators (MRs) of progression to aggressive disease (forkhead box protein M1 and centromere protein F), inferred by the Master Regulator Inference algorithm (MARINa) [7,[12][13][14][15], and experimentally validated both in mouse and in human tissue. However, the analysis also showed that 30% of the programs are not conserved, including those representing a few PC-related genes that would thus be unlikely to produce patient-relevant results if studied or targeted in a murine context.…”

“…This is accomplished by measuring the enrichment of over-and underexpressed genes in positively regulated and repressed targets in the regulon of every possible regulator protein represented in the interactome, thus providing an accurate and extremely robust predictor of the differential activity of a regulator. This has allowed the discovery of key functional drivers of tumorigenesis and drug sensitivity, including single regulators [13,15,[41][42][43], synergistic regulator pairs [4,12,14], and additive mechanisms that could not have been elucidated using traditional methods. Indeed, virtually none of the regulators that were experimentally validated were significantly differentially expressed at the RNA level and yet they were confirmed as individual or synergistic phenotypic drivers following identification by regulatory network analysis, thus elucidating novel mechanisms of disease initiation/ progression [4,12,13,[41][42][43][44][45][46], chemosensitivity [15,28], and normal physiologic regulation [14].…”

“…This has allowed the discovery of key functional drivers of tumorigenesis and drug sensitivity, including single regulators [13,15,[41][42][43], synergistic regulator pairs [4,12,14], and additive mechanisms that could not have been elucidated using traditional methods. Indeed, virtually none of the regulators that were experimentally validated were significantly differentially expressed at the RNA level and yet they were confirmed as individual or synergistic phenotypic drivers following identification by regulatory network analysis, thus elucidating novel mechanisms of disease initiation/ progression [4,12,13,[41][42][43][44][45][46], chemosensitivity [15,28], and normal physiologic regulation [14]. Lately, we have successfully extended these methodologies to the study of neurological, neurodevelopmental, and stem cell phenotypes [35,42,47], and, more recently, to neurodegenerative phenotypes, resulting in a series of manuscripts, currently in review, where we report on the elucidation and experimental validation of novel genes mediating neurotoxicity in ALS [48], as well as biomarkers of AD progression [9].…”

Phage display discovery of novel molecular targets in glioblastoma-initiating cells

“…21 Screens for GIC regulators have included gene expression profiling, chemical screens or RNA interference. [45][46][47] Recently, we reported the use of cell-based aptamer screening to identify several aptamers that selectively identify self-renewing, tumorigenic cells. 48 Methods for identifying and subsequent targeting of target molecules are limited by cost, relatively small numbers of pre-determined antigen targets, and limited utility in cells and tissues in their native state.…”