G-quadruplex stabilizer CX-5461 effectively combines with ionizing radiation to selectively target ATRX-deficient malignant glioma

Mutational inactivation of ?-thalassaemia/mental retardation X-linked (ATRX) represents a defining molecular feature in large subsets of adult and pediatric malignant glioma. ATRX deficiency gives rise to abnormal G-quadruplex (G4) DNA secondary structures at GC-rich regions of the genome, altering chromatin accessibility and enhancing DNA damage. Building on earlier work, we sought to assess the extent to which pharmacological G4 stabilization selectively enhances DNA damage and cell death in preclinical models of ATRX-deficient glioma. In this study, we assessed the extent to which G4 stabilization impacted genome-wide deposition of H3.3 in patient-derived glioma stem cells (GSCs). In order to evaluate the overlap of these H3.3 deposition sites with regions of the genome that bind ATRX, we performed cleavage under targets and tagmentation (CUT&Tag) for ATRX using GSC line TS 543. Our analyses show that G4 stabilizer CX-541 disrupts H3.3 deposition at regions of the genome that frequently bind ATRX. Global genomic profiling analyses of ATRX CUT&Tag sequencing data for patient-derived glioma stem cell line (GSC) TS 543, which was conducted in triplicates.