Elucidating Cell Diversity and Functions of Human Brain Borders in Alzheimer’s Disease

Abstract

AbstractBackgroundEmerging evidence shows that the brain border regions act as a functional neuro‐immune interface to conduct essential immune surveillance and immune defense1. The dysfunction of border immunity contributes to aging, microglial inflammatory response, and neurodegeneration2‐3.MethodWe conducted single nuclei multiome to simultaneously profile gene expression and open chromatin of dissected postmortem human brain borders from aged individuals with and without Alzheimer’s Disease (AD) (n = 32). We further generated border cell models from iPSCs and postmortem leptomeningeal cells to understand the effects of genetic and environmental factors on border cells.ResultWe detect diverse cell types at the brain borders, including unique endothelial, mural, immune, and fibroblast subtypes. Border‐associated macrophages (BAMs) display differential gene expressions from microglia and express AD risk genes, as nominated by genome‐wide association studies (GWAS). We discover cell‐type‐specific differentially expressed genes in AD individuals, particularly fibroblasts and BAMs. We identify gene regulatory networks and master regulators of specific border cell states. Human cell models of leptomeningeal cells display the signature of ex vivo AD fibroblasts upon amyloid‐β treatment, and iPSC‐derived choroid plexus models carrying the APOE4 risk alleles demonstrate differentially expressed genes related to immune and fibrotic response. Lastly, we explore ligand‐receptor interactions within the border niche and observe increased intercellular activities and altered communication patterns at AD brain borders.ConclusionOur study establishes a molecular map of human border cell types and reveals the functional effects of AD risk factors on brain border cells, providing significant insight into the border immune and fibrotic responses in AD pathogenesis.