Applications of Spatial Transcriptomics in Ischemic Stroke Research

Acute ischemic stroke is a complex disorder in which the damage goes beyond neuronal loss and involves dynamic responses from glial, vascular, stromal, and immune cells. Spatial transcriptomics (ST) has become a powerful tool to study these processes by preserving tissue architecture while revealing detailed gene expression patterns. This review describes how ST has advanced the understanding of cellular changes after stroke, focusing on microglia, astrocytes, and oligodendrocytes to showcase the complexity of stroke pathobiology. Research has shown that the glial cells adopt different states depending on location and time, influencing both harmful and protective outcomes, such as inflammation, blood-brain barrier damage, remyelination, and tissue repair. By combining ST with single-cell and multiomics approaches, new therapeutic targets have been identified, including different types of activated glial states, and key signaling pathways involved in glial communication. Despite the recent progress in ST, challenges remain, particularly the need for multi-time point analyses, three-dimensional reconstructions and standardized data sets that can move the field closer to clinical applications. Future reference atlases, together with experimental validation, will be essential for developing precise, cell-targeted therapies. This review summarizes the results from the most recent ST studies and highlights the possible applications of spatial approaches to improving stroke research and therapy.