ATRX inactivation disrupts global chromatin state and topology to dysregulate neurodevelopmental pathways in glioma pathogenesis.

Mutational inactivation of the chromatin regulator gene ATRX (a-thalassemia mental retardation X-linked) represents a defining molecular abnormality in multiple cancer types. Recent findings suggest that the multifaceted consequences of ATRX deficiency on global chromatin landscapes fundamentally alter cellular differentiation and other complex phenotypes relevant to cancer, particularly in neuroepithelial and mesenchymal lineages. To comprehensively define ATRX-deficient epigenomic abnormalities and their transcriptional and phenotypic sequelae in a disease-relevant context, we conducted an array of high-throughput epigenome mapping studies in isogenic Atrx- and Atrx+ murine neuroepithelial progenitors (mNPCs). These investigations revealed that Atrx loss widely impacts 3D chromatin architecture and looping, with specific changes in topologically associating domains (TADs) and CCCTC-binding factor binding sites overlying neurodevelopmental gene sets. TAD shifts closely approximated disrupted large histone H3K9me3-marked laminin-associated domains, along with reprogrammed enhancer/superenhancer regions at neurodevelopmental effectors, including a novel regulator of cell migration, Slitrk6, and the cancer-implicated HoxA cluster. Pharmacologic inhibition of HOXA-PBX binding selectively impaired the in vivo growth of patient-derived ATRX-deficient glioma stem cells. Taken together, our findings reveal that rewiring of chromatin topology and heterochromatin structure promotes cancer-associated phenotypes in ATRX-deficient glioma through induction of therapeutically targetable neurodevelopmental gene expression.