Single‐Cell RNA Sequencing and Spatial Multiomics Unveil Microglia–Mural Interactions Underlying Notoginsenoside R1 Against Ischemic Stroke

ABSTRACT Ischemic stroke remains a global clinical challenge. Notoginsenoside R1 (NGR1), derived from the clinically valued herb Panax notoginseng , shows therapeutic potential but its mechanisms remain unclear. Using exploratory single‐cell RNA‐seq and spatial multiomics (Spatial‐seq/SMALDI‐MSI), our analyses suggested that NGR1 reversed inflammatory mural phenotypes to restore vascular function in the middle cerebral artery occlusion model. Inspired by this inflammatory phenotype transformation, analyses suggested that NGR1 rewired microglia‐mural cell crosstalk by reducing the ischemia‐associated microglial subtype ( Adam8 hi ) while expanding the protective Socs3 hi subtype. RNA‐velocity and diffusion map analyses suggested an NGR1‐associated shift in microglial transcriptional state distribution toward the Socs3 hi state, with the lipid transporter Abca9 identified as a putative driver gene. Consistently, SMALDI‐MSI showed that NGR1 reprogrammed metabolic profiles in ischemic brains. Depleting Abca9 in microglia abolished NGR1's benefits both in vitro and in vivo. NGR1 directly binds to FOXO1, which regulates a broader transcriptional program with Abca9 as a functionally supported component, to modulate microglial inflammatory response. These findings suggest that microglia‐mural interactions contribute to NGR1's protection and identify the broader FOXO1‐associated program with ABCA9 as a potential functionally supported component for stroke therapy.