Microglia aggregates define distinct immune and neurodegenerative niches in Alzheimer's disease hippocampus.

In Alzheimer's disease (AD), microglia show strong associations with amyloid-β (Aβ) and tau pathology, forming cellular aggregates such as Aβ plaque-associated microglia (PaM). Using high-content neuropathology, we found another type of microglial aggregates, morphologically distinct and not associated with Aβ plaques, mainly localised in the pyramidal layer of the CA2/CA1 human hippocampal subfields of AD patients, namely Coffin-like microglia (CoM). This study aims to define the morphological, pathological and molecular signatures of hippocampal PaM and CoM in AD patients and their implication in disease progression. We mapped and profiled PaM, CoM and their neuropathological and astrocytic microenvironment using Nanostring GeoMx Deep Spatial Profiling (DSP), multiplex chromogenic and confocal microscopy in AD hippocampal post-mortem samples. Key markers and result s were validated in a collection of AD, DLB and age-matched control samples. CoM, found attached to tau tangles and neurons with phosphorylated α-synuclein accumulations, displayed specific protein and transcriptomic signatures associated with STING, protein degradation, TGF-β, and NF-κB signalling pathways. In contrast, PaM and PaM-astrocyte signatures were associated with complement system pathways, ErbB signalling, metabolic and neurodegenerative activities. While no direct association of CD8 + T cells with either PaM or CoM was observed, CD163 + perivascular macrophages were frequently found incorporated into PaM. This study provides new insights into the molecular characteristics of microglia and their association with astrocytes and infiltrating immune cells to delineate specific neurodegenerative hotspots in AD and related dementia and highlights their prominent role in hippocampal deterioration.