Whole-brain mRNA imaging unveils the dynamics of neuroinflammation after stroke

The dynamic role of neuroinflammation in diverse neurological disorders is still poorly characterized but could represent a promising avenue for therapeutic interventions. Here we aimed at characterizing brain-wide response of microglia to ischemic stroke in mouse. Microglia, the frontline responders to ischemic stroke, is known to exhibit diverse morphology and gene expression in response to diverse stimuli and depending on tissue context, yet how their activation signature propagates across the brain in response to local stroke has remained unknown. Here we established a whole-brain three-dimensional (3D) mRNA imaging method to map changes in microglia activation in the context of other injury associated changes. Brains from female and male mice were subjected to permanent middle cerebral artery occlusion (pMCAO), and labelled for diverse microglia (i.e. Iba1, Hexb) and vascular markers (CD31, SM22a) at mRNA and protein level. Following tissue clearing, intact brains were visualized using light-sheet fluorescent microscopy. We show local accumulation of activated microglia and rearrangement of cerebral vasculature at the stroke site 7 days after occlusion. Stroke led to propagation of the inflammatory signal to distant brain regions, indicating broad effects that are not confined to the lesioned area. This study introduces a novel 3D imaging platform to track microglia activation during disease progression and could be utilized in preclinical pharmacological research.