Complement biosynthesis in human brain: Insights from single-nucleus transcriptomics of hippocampus

Complement is a key contributor to neuroinflammation, driving pathology in neurodegenerative diseases (NDDs); however, little is known about the source of complement in brain. Effective targeting of complement in NDDs requires understanding of its source; in particular, which brain cells express complement genes, how expression is regulated and how expression changes in disease.

To address this knowledge gap, we identified and integrated single-nucleus RNA sequencing (snRNA-seq) datasets from 398,097 nuclei across 48 hippocampal samples from non-demented brains to create a comprehensive transcriptomic atlas of complement gene expression ("complementome") in healthy brain. Expression levels of genes encoding complement components, receptors, and regulators were analysed across different brain cell types and the impact of sex and age on complement gene expression tested. To test impact of disease, we generated a further atlas from datasets comprising 11 non-demented and 12 Alzheimer’s disease (AD) patient hippocampi to assess changes in complement gene expression in AD.

All glial cells in the non-demented hippocampus expressed complement genes. C1Q A/B/C genes were exclusively expressed in microglia, while C3 was highly expressed in microglia and astrocytes. Notably, C3 expression defined a subset of pro-inflammatory microglia. Complement receptor encoding genes ( C3AR1 , C5AR2 , ITGAM , ITGAX , ITGB2 , VSIG4 ) were predominantly expressed in microglia, while neurons expressed a set of brain-specific putative receptors ( NPTX 1/2 , NPTXR , NRP1 ). Endothelial cells abundantly expressed key regulators ( CD46 , CD55 , CD59, CFH ), while neurons and OPCs expressed a set of putative regulators ( CSMD 1/2/3 , and SUSD4 ). Astrocytes abundantly expressed CLU . Cell type-specific gender differences included higher expression of C1Q A/B/C , C1R , C1S in female microglia and higher expression of ITGAM and ITGAX in male microglia. Generally higher complement gene expression was seen in older donors. Compared to controls, AD microglia showed higher expression of C1QB and C3 , and AD astrocytes showed higher C1S and C3 expression. Expression of ITGAX was elevated in AD microglia compared to controls, while many AD cell types demonstrated reduced expression of brain-specific putative receptors.

Defining the complementome in non-demented hippocampus provides a baseline for exploration of brain complement expression. Complement expression is upregulated in AD, likely contributing to neuroinflammation and highlighting its potential as a therapeutic target.

Graphic abstract