Integrating single-cell and spatial transcriptomics to reveal the spatiotemporal dynamics of retinal cells during ischemia-reperfusion injury progression in rats

Retinal ischemia–reperfusion (I/R) injury is a key pathological process in retinal-associated diseases such as glaucoma. However, the spatiotemporal dynamics and cell interactions during this injury are not fully understood. This study integrated single-cell RNA sequencing and spatial transcriptomics to map retinal cell responses in a rat I/R injury model at acute, subacute, and chronic stages. We identified 14 cell populations and tracked gene expression changes over time. Retinal ganglion cells (RGCs) showed activation of apoptotic, autophagic, and oxidative stress pathways within 24 h. Spatial analysis revealed RGCs co-localized with Müller glial and microglial cells in the optic nerve and inner retina, with RGC death driven by ligand-receptor interactions (e.g., Ncam1-Ncam1, App-Sorl1). Transcription factors (Sox9/Sox8) in Müller cells regulated TNF/JAK-STAT signaling, while Alzheimer’s-related Mapt exhibited spatiotemporal specificity in RGCs, suggesting shared neurodegenerative pathways. This study constructed a panoramic spatiotemporal dynamic map of retinal I/R injury progression, providing important clues for the development of potential therapeutic targets for glaucoma and related retinal diseases.