Intro: Complement contributes significantly to pathophysiology in many neurodegenerative diseases (NDDs) including Alzheimer’s Disease (AD); yet, the source of complement in the brain is poorly understood. Targeting complement effectively in NDDs requires understanding complement expression in the healthy brain, how it changes and the effect of altered expression on the cell populations in the brain.
Objectives: We aimed to characterise which cell types in the brain express complement in the healthy brain, how expression is altered in AD, and the functional implications of any alterations.
Methods: We integrated single-nucleus RNA sequencing datasets including 606,265 cells across 97 donor frontal cortices (60 AD: 36 male, 24 female; 37 controls: 23 male, 14 female). Differential expression analysis (DEA) using the Wilcoxon rank sum test (Bonferroni adjusted) was performed to assess the effects of AD pathology, sex, and age on complement gene expression across nine cell types. Protein-protein interaction networks were inferred with STRING, and cell-cell communication (CCC) analyses using CellChat examined complement-related signalling changes in AD.
Results: Complement genes displayed cell-type–specific expression in healthy and AD cortices. DEA identified significant AD-associated changes in complement gene expression, most prominently in microglia, where C1QA/B/C, CFD, C3, C5, ITGAX, ITGB2 and VSIG4 were strongly upregulated. STRING placed these genes in an interacting protein cluster enriched for synaptic pruning and immune activation. Additional complement genes (C1R, C1S, C7, SERPING1, SRPX2) were upregulated in endothelial cells, fibroblasts, and pericytes – cells linked to vasculature. CCC revealed widespread alterations in immune signalling mediated by complement proteins especially in astrocytes and microglia – including CD23, CD40, ICAM and vitronectin signalling – highlighting complement dysregulation affects multiple immune pathways within glial populations. DEA also showed greater loss of complement regulator expression in females in AD, and that dysregulation is most severe in younger AD cases.
Conclusion: Our comprehensive atlas of complement expression in AD and control frontal cortex demonstrates that AD profoundly disrupts complement homeostasis. Dysregulation is strongest in microglia and linked to enhanced complement-mediated synaptic pruning and immune responses. Widespread alterations in complement-mediated intercellular signalling in glial cells indicates glia are key to understanding how complement contributes to AD.