Mus musculus Raw sequence reads. Mus musculus

Single-cell RNA sequencing analyses in recent studies have elucidated microglia characteristics associated with inflammatory conditions and neurodegeneration. Nevertheless, studies on the heterogeneity of microglia subpopulations induced by chronic cerebral hypoperfusion (CCH) are limited. To further characterize the heterogeneity of microglial responses towards CCH, we established a mouse bilateral common carotid artery stenosis model and performed single-cell RNA sequencing of mouse microglia. We identified inflammation-associated microglia (classically activated microglia and demyelination microglia), remyelination microglia, and canonical microglia. We found that under the condition of chronic cerebral hypoperfusion, the expression of canonical microglia was downregulated, the expression of inflammation-associated microglia was increased, and the expression of remyelination microglia was increased. Moreover, the novel cell subset, Klf2_Microglia, which may exert unique anti-inflammatory effects under CCH. Our study may provide new research perspectives and therapeutic ideas for chronic cerebral hypoperfusion and neuroinflammatory diseases.