Exploring cellular heterogeneity: single-cell and spatial transcriptomics of Alzheimer's disease brains and iPSC-derived microglia.

BACKGROUND

Microglia, the brain’s resident immune cells, play a pivotal role in Alzheimer’s disease (AD) pathogenesis. These cells exhibit diverse transcriptional states in response to neuroinflammatory stimuli, and characterizing these states is essential for understanding AD mechanisms.

METHODS

We integrated single-cell and spatial transcriptomic datasets from multiple cohorts and brain regions, encompassing both experimental models and human tissues. Findings were validated through immunostaining of human brain samples.

RESULTS

Our comprehensive atlas revealed pronounced heterogeneity among microglial states, with disease-associated microglia (DAM) significantly enriched in AD brains compared to controls. Spatial transcriptomics and immunohistochemistry demonstrated that DAM predominantly localize to external cortical layers and near amyloid plaques, whereas homeostatic microglia are more abundant in internal cortical layers and distal regions. Immunofluorescence staining for P2RY12 and CD68 confirmed these spatial distributions.

CONCLUSION

By harmonizing single-cell and spatial transcriptomics, we provide a detailed atlas of microglial diversity, highlighting regional and pathological specificity of microglial states in AD. SIGNIFICANCE: This work advances prior studies by mapping microglial transcriptional states across multiple human cohorts and experimental contexts, integrating spatial data to reveal novel anatomical patterns. The enrichment of DAM in external cortical layers and homeostatic microglia in internal layers represents a previously unreported finding with potential therapeutic implications. While not exhaustive of all microglial datasets, this study establishes the first integrated reference combining single-nucleus and spatial transcriptomics, underscoring the importance of linking microglial diversity to AD neuropathology and brain architecture.