Ischemic stroke is a leading cause of death and long-term disability worldwide. Current recanalization therapies are limited by a narrow therapeutic window, and many patients still suffer from persistent hypoperfusion due to post-ischemic microvascular dysfunction even after successful reperfusion. There is an urgent need for novel strategies that restore microcirculatory homeostasis in the ischemic penumbra.
Traditional Chinese Medicine (TCM) has emerged as a rich source for neuroprotective drug discovery. Panax notoginseng, a classic TCM herb known for “promoting blood circulation and resolving stasis”, has attracted interest as a source of potential neuroprotective compounds. Notoginsenoside R1 (NGR1), one of its principal bioactive saponins, has shown neuroprotective activities including anti-inflammation, anti-apoptosis, and microcirculation improvement. However, its cell-type-specific mechanisms and spatial effects in the ischemic brain have remained largely unclear.
A research team led by Drs. Yanrong Zheng, Shengshuang Chen, Jie Liao, and Xiaohui Fan describes a new study applying an integrated spatial multiomics strategy to systematically dissect the mechanisms of NGR1 against cerebral ischemia. The team combined single-cell RNA sequencing (scRNA-seq), spatial transcriptomics (Spatial-seq), and spatial metabolomics (SMALDI-MSI) in a mouse model of middle cerebral artery occlusion (MCAO).
The researchers first demonstrated that systemic NGR1 administration dose-dependently reduced cerebral infarct volume and alleviated neurological deficits in MCAO mice. NGR1 treatment also improved 7-day survival. In the acute injury measures examined, both NGR1 and the positive control edaravone showed neuroprotective effects. Across 37,212 captured single cells, the team identified 15 brain cell lineages. Integrative analysis with spatially resolved transcriptomic profiles showed that NGR1-associated shifts in the relative representation of several cell types toward the sham pattern, most prominently in mural cells and microglia — two cell types critical for cerebral blood flow regulation and neuroinflammation, respectively.
Further analysis suggested NGR1-associated remodeling of post-ischemic mural cell transcriptional states, with shifts away from inflammatory profiles. Functional experiments demonstrated that NGR1 alleviated excessive pericyte contraction in vitro and increased α-SMA-positive vascular coverage in vivo. Consistently, NGR1 treatment improved cerebral blood perfusion in the ischemic penumbra. In parallel, NGR1 treatment was associated with lower relative representation of the ischemia-associated Adam8hi subtype and higher relative representation of the Socs3hi subtype. Cell-cell communication analysis suggested NGR1-associated changes in predicted microglia–mural signaling networks, consistent with a shift toward more homeostatic communication patterns.
To investigate potential molecular regulators of NGR1-associated microglial states, the team performed RNA velocity analysis and functional validation. The lipid transporter Abca9 was identified as a putative driver gene associated with the Socs3hi transcriptional state. In vitro, ABCA9 knockdown diminished NGR1-mediated suppression of IL-1β and its effect on pericyte contraction in co-culture. In vivo, Abca9 knockdown was associated with larger infarcts and worse neurological scores in NGR1-treated mice, supporting a functional contribution of ABCA9 to the observed protective effects. Mechanistically, NGR1 directly binds to FOXO1, and FOXO1 perturbation altered ABCA9 expression, supporting ABCA9 as a functionally relevant component of a broader NGR1-responsive FOXO1-associated transcriptional program.
“Our findings bridge neuroinflammation mitigation and vascular stabilization through a microglial FOXO1-associated program, with ABCA9 as a functionally supported component,” the authors noted. “This study not only provides single-cell resolved insights into the mechanism of notoginsenoside R1, but also identifies potential therapeutic targets for precise cerebral blood flow regulation in the context of cerebral ischemia.”
The authors acknowledge several limitations, including the lack of independent library-level replication for the exploratory scRNA-seq analysis, the restriction of the mechanistic multiomic analyses to the acute 24-h phase, and the need for validation in human neurovascular systems.
iMetaMed
Experimental study
Animals
Single-cell RNA sequencing and Spatial Multiomics Unveil Microglia-Mural Interactions underlying Notoginsenoside R1 against Ischemic Stroke
3-Nov-2026
Prof. Xiaohui Fan and Prof. Jie Liao are listed in the Editorial Board Members of iMeta. All other authors declare no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.