Comparing the spatial transcriptomic difference of the protective effect between Panax notoginseng and Panax ginseng against acute stroke with Spatial-seq 2.0

This study investigates the therapeutic effects of Panax notoginseng saponins (PNS) and Panax ginseng saponins (PGS) on acute ischemic stroke using an optimized spatial transcriptomics technology, Spatial-seq 2.0. The aim is to provide spatial insights into their functional differences and mechanisms. A permanent middle cerebral artery occlusion (pMCAO) model was established in C57BL/6 mice. Animals were treated with low and high doses of PNS and PGS. Neurological scores, infarct volumes, survival rates, and histological alterations were analyzed. Spatial-seq 2.0 was utilized to capture the transcriptomic profiles of brain regions, focusing on ischemic penumbra. Differentially expressed genes were validated using qRT-PCR, and GO/KEGG enrichment analysis was conducted. Both PNS and PGS significantly reduced infarct volume, improved neurological function, and attenuated neuronal apoptosis following acute ischemic stroke injury. Spatial transcriptomic analysis identified both shared and distinct molecular responses, with PNS preferentially regulating actin cytoskeleton-related pathways, consistent with its traditional Chinese medicine (TCM) function of "activating blood" , whereas PGS mainly modulated mitochondrial energy metabolism, which is in line with its "replenishing qi" property. These transcriptomic findings were further supported by Western blot analysis. Collectively, our findings provide molecular evidence that may help explain the pharmacological characteristics of PNS and PGS and offer new insights into the scientific basis of the TCM strategy of "replenishing qi and activating blood" for ischemic stroke.PNS and PGS exhibit differential yet complementary effects in stroke therapy, consistent with their traditional medicinal roles. The spatially resolved transcriptomics approach provided novel insights into their mechanisms, underscoring the potential of Spatial-seq for TCM research.