Single-cell Multiomics Integration of Microglia Across Alzheimer’s Disease Continuum

초록

The brain has historically been considered an immune-privileged organ, characterized by a dense network of synaptic connections. Microglia, the resident innate immune cells of the central nervous system, exhibit remarkable heterogeneity and are essential for preserving synaptic integrity and removal of synaptic debris. Recent advancements in single-cell technologies have illuminated a functional continuum of microglial states—ranging from neuroprotective to neurodegenerative—closely linked to individual variability in disease susceptibility and progression, particularly in Alzheimer’s disease (AD). In this study, we constructed a comprehensive single-cell multiomics atlas of microglia by integrating single-cell transcriptomics and proteomics, augmented with individualized morphometric parameters. Utilizing our custom-developed single-cell microHOLD proteomic platform, we resolved proteomic alterations at the single-cell level across microglial subsets derived from models spanning the AD continuum. Spatial localization of individual microglial cells was achieved through integration with MERFISH-based transcriptomic data encompassing 2.8 million cells. Additionally, single-cell morphometric profiling was performed to correlate microglial functional states with dynamic morphological transitions along the course of AD pathology. Our integrated single-cell multiomics map reveals disease-associated microglial functional heterogeneity and morphological specialization, offering new insights into region-specific microglial roles in the AD brain and highlighting potential targets for therapeutic intervention.