Integrating spatial and single-cell transcriptomics to characterize the molecular and cellular architecture of the ischemic mouse brain

TL;DR: This study provides a detailed molecular and cellular characterization of the peri-infact area in a murine stroke model and revealed Lgals9 as potential treatment target that warrants further investigation, highlighting the utility of integrating single-cell and spatial transcriptomics to characterize cellular changes in disease states and to identify potential therapeutic targets.

Abstract: Neuroinflammation is acknowledged as a pivotal pathological event after cerebral ischemia. However, there is limited knowledge of the molecular and spatial characteristics of nonneuronal cells, as well as of the interactions between cell types in the ischemic brain. Here, we used spatial transcriptomics to study the ischemic hemisphere in mice after stroke and sequenced the transcriptomes of 19,777 spots, allowing us to both visualize the transcriptional landscape within the tissue and identify gene expression profiles linked to specific histologic entities. Cell types identified by single-cell RNA sequencing confirmed and enriched the spatial annotation of ischemia-associated gene expression in the peri-infarct area of the ischemic hemisphere. Analysis of ligand-receptor interactions in cell communication revealed galectin-9 to cell-surface glycoprotein CD44 (LGALS9-CD44) as a critical signaling pathway after ischemic injury and identified microglia and macrophages as the main source of galectins after stroke. Extracellular vesicle–mediated Lgals9 delivery improved the long-term functional recovery in photothrombotic stroke mice. Knockdown of Cd44 partially reversed these therapeutic effects, inhibiting oligodendrocyte differentiation and remyelination. In summary, our study provides a detailed molecular and cellular characterization of the peri-infact area in a murine stroke model and revealed Lgals9 as potential treatment target that warrants further investigation. The transcriptomic landscape was characterized at single-cell and spatial resolution of the ischemic mouse brain. Editor’s summary Knowledge of the spatial distribution of nonneuronal cells at the infarct site could help to understand processes that determine regeneration after ischemic stroke. Han and colleagues combined spatial and single-cell transcriptomics to map gene expression and cell distribution in the ischemic mouse brain. Bioinformatic analysis showed that galectin (LGAL) signaling by microglia and macrophages was increased in ischemic mice. Treatment with LGALS9 promoted remyelination by oligodendrocytes and ameliorated stroke recovery in mice. These results highlight the utility of integrating single-cell and spatial transcriptomics to characterize cellular changes in disease states and to identify potential therapeutic targets. —Daniela Neuhofer