Open Access

Paula Sanchez-Molina, Dennis-Dominik Rosmus, Dillon Brownell, Mert Meral, Cavanagh Gohlich, Aditya Pratapa, Yaser Peymanfar, Alyssa Whitley, Yue Hou, Nadezhda Nikulina, Alina Bogachuk, Ellen Lara Bouchard, Aude Chiot, Heidrun Kuhrt, Peter Wieghofer, Randall Woltjer, Fabian Svara, Oliver Braubach, Bahareh Ajami

• Disease-associated microglial states are thought to contribute to Alzheimer’s disease (AD) progression, but characterizing them and their relationships to pathology remains challenging. Here we introduce CODEX-CNS—a multiplexed protein imaging technology with a custom data analysis pipeline for use in human brain samples. We profiled 704,706 cells in samples from the frontal cortex of 8 people with AD and 8 healthy controls and mapped features including blood–brain barrier, meningeal components and cell–cell interactions within the same tissue sections. Amongst the myeloid cell populations we identified, we found a border-associated macrophage-like microglial subset associated with aging. Further classifying myeloid cell subsets based on their spatial neighborhood, we identified a border-associated macrophage-like microglial subpopulation that was associated significantly with dense amyloid-β plaques, which we termed human plaque-associated microglia. This work offers insights intoDisease-associated microglial states are thought to contribute to Alzheimer’s disease (AD) progression, but characterizing them and their relationships to pathology remains challenging. Here we introduce CODEX-CNS—a multiplexed protein imaging technology with a custom data analysis pipeline for use in human brain samples. We profiled 704,706 cells in samples from the frontal cortex of 8 people with AD and 8 healthy controls and mapped features including blood–brain barrier, meningeal components and cell–cell interactions within the same tissue sections. Amongst the myeloid cell populations we identified, we found a border-associated macrophage-like microglial subset associated with aging. Further classifying myeloid cell subsets based on their spatial neighborhood, we identified a border-associated macrophage-like microglial subpopulation that was associated significantly with dense amyloid-β plaques, which we termed human plaque-associated microglia. This work offers insights into myeloid cell heterogeneity in AD and provides a new spatial approach to characterizing brain cells at the single-cell protein level.…