Deep spatial phenotyping of microglial populations and pathological features in Alzheimer’s disease brains using CODEX Multiplexed Imaging

Recent high‐throughput transcriptomics and proteomics analysis have shown a remarkable heterogeneity of microglia phenotypes across various disease conditions. Differently from neurons, microglia appearance can be characterized as a continuum between ramified and amoeboid morphologies. The transcriptional and proteomic profiles associated to each degree of morphology are potentially multiple and dependent on the healthy/pathological conditions in consideration with sex, anatomical area of the brain and disease stage. While single‐cell RNA sequencing (scRNA‐seq) has been instrumental in revealing microglia sub‐populations, it is lacking in spatial information and phenotypic characterization. The scarcity of fresh human brain tissue imposes a bottleneck for RNA‐seq studies, while paraffin‐embedded tissues are widely available in most brain banks. CODEX multiplexed imaging technology permits a deep characterization of microglial cells preserving their morphology and avoiding cell activation by aggressive sample preparation methods as occurs in tissue homogenates. Moreover, we can discriminate the immune cells in brain blood vessel from those in the parenchyma.