A spatiotemporal immune atlas of subarachnoid hemorrhage from single-cell and spatial transcriptomics [ST]

Early brain injury (EBI) within the first 72 hours largely determines outcome and shaped by immune and inflammatory responses. Here, we integrated single-cell RNA sequencing (scRNA-seq) of CD45+ cells with spatial transcriptomics (ST) in a murine SAH model to chart the immune landscape at 24 and 72 hours.

Across macrophages, neutrophils, and microglia, we observed pronounced transcriptional remodeling, resolving five macrophage subsets, four neutrophil subsets, and eight microglial subsets. Neuroinflammation-associated states included macrophage subsets M_01(Spp1⁺, Lgals1⁺), M_03 (Isg15⁺, Ifit3⁺), M_04 (Csf3r⁺, Clec4e⁺); neutrophil subsets N_01 (Spp1⁺, Thbs1⁺), N_02 (Ly86⁺, Trem2⁺); and microglial subsets MG_01 (Jun⁺, Fos⁺); MG_03 (Spp1⁺, Lpl⁺); MG_04 (C1qa⁺, Ctsd⁺).