Spatial Transcriptomic Analysis Reveals HDAC Inhibition Modulates Microglial Dynamics to Protect Against Ischemic Stroke in Mice

ABSTRACT Ischemic stroke significantly contributes to global morbidity and disability through a cascade of neurological responses. Microglia, the immune modulators within the brain, exhibit dual roles in exacerbating and ameliorating ischemic injury through neuroinflammatory and neuroprotective roles, respectively. Despite emerging insights into microglia's role in neuronal support, the potential of epigenetic intervention to modulate microglial activity remains largely unexplored. We have previously shown that sodium butyrate, a histone deacetylase inhibitor (HDACi) epigenetically regulates the inflammatory response of microglia after ischemic stroke, and this study was aimed at characterizing the transcriptomic profiles of microglia and their spatial distribution in the stroke brain following HDACi administration. We hypothesized that the administration of HDACi epigenetically modulates microglial activation and a region‐specific microglial phenotype in the stroke brain, shifting their phenotype from neurotoxic to neuroprotective and facilitating neuronal repair in the ischemic penumbra. Utilizing a rodent model of stroke, spatial transcriptomics and 3D morphometric reconstruction techniques were employed to investigate microglial responses in critical penumbral regions following HDACi administration. We found HDACi significantly altered the microglial transcriptomic landscape involving biological pathways of neuroinflammation, neuroprotection, and phagocytosis, as well as morphological phenotype, promoting a shift toward reparative, neurotrophic profiles within the ischemic penumbra. These changes were associated with enhanced neuronal survival and reduced neuroinflammation in specific regions in the ischemic brain. By elucidating the mechanisms through which HDACi influences microglial function, our findings propose therapeutic avenues for neuroprotection and rehabilitation in ischemic stroke, and possibly other neurodegenerative conditions that involve microglia‐mediated neuroinflammation.