Microglial function alterations during healthy ageing and canine cognitive dysfunction revealed by single-nucleus and spatial transcriptomics

Abstract Canines, which spontaneously develop Alzheimer's disease (AD) -like pathology with age, serve as valuable translational models for studying AD. However, the cellular molecular functions of the canine brain in healthy ageing and/or canine cognitive dysfunction (CCD) have not yet been studied. Here, we present a multiregional healthy canine brain ageing atlas using snRNA-seq, alongside a CCD versus nonCCD brain atlas generated using both snRNA-seq and Stereo-seq. Cellular heterogeneity analysis during healthy brain ageing revealed that glial cells undergo the most pronounced alterations, with previously uncharacterised ageing-related subtypes identified in microglia and astrocytes that contribute to myelin synthesis. This analysis also identified and validated ZEB1 as a previously unrecognised transcription factor regulating oligodendrocyte differentiation, with expression progressively declining with age. Pathogenetic analysis of CCD revealed that the interaction between microglial C1QA and CRT in dentate gyrus granule cells is a critical mediator of synaptic loss. Furthermore, compared with microglia from normally ageing canines, the canine CCD exhibited a significant decrease in the ability to metabolise amyloid precursor protein in microglia. Overall, this study provides a single-nucleus and spatial transcriptomic atlas of the ageing and CCD brain, offering insights into molecular features underlying cognitive dysfunction.