NAT10-Dependent N4-acetylcytidine (ac4C) on R-loops Drive Glioblastoma Tumorigenesis and Stemness [H3K27ac]

R-loop remodelling dynamically regulates chromatin states and gene expression; however, its exploitation by cancer stem cells to sustain self-renewal and malignancy remains poorly understood. In this study, we found that glioblastoma stem cells (GSCs) maintain a highly active R-loop state compared to their differentiated progeny and normal human stem cells. Genome-wide mapping via RR-ChIP-seq revealed cell-specific enrichment and spatial accumulation of R-loops at promoter-proximal regions in GSCs, correlating with active transcription and open chromatin states. To identify key regulators, we profiled the R-loop interactome and identified N-Acetyltransferase 10 (NAT10), an established RNA ac4C-modifying enzyme, as a high-affinity R-loop-binding protein in GSCs. Driven by transcriptional activation via OLIG1, NAT10 is overexpressed in both GSCs and GBM. ac4C RIP-seq on R-loop RNA revealed abundant ac4C-modified R-loops that regulated the GSC genome. Mechanistically, NAT10 catalyzes widespread ac4C deposition on the RNA stand of R-loops, stabilizing promoter-associated R-loops, and facilitating an open chromatin state to sustain GSC self-renewal through controlling key stemness regulators such as the transcription factor EGR1. NAT10 knockdown suppressed GSC proliferation and maintenance in vitro and attenuated GBM progression in orthotopic xenograft models in vivo. Pharmacological inhibition of NAT10/ac4C-modified R-loops using the small-molecule inhibitor Remodelin phenocopied NAT10 genetic targeting, demonstrating therapeutic promise for targeting this axis in GBM.