In situ Complementomics enables spatial complement activation profiling and identification of therapeutic targets across human tissues

Complement activation is increasingly recognized as a driver of inflammation in diverse human diseases, prompting the development of targeted inhibitors across the cascade. However, despite compelling preclinical evidence, clinical success has been inconsistent, highlighting the need for tools that can dissect complement activity within its spatial and cellular context. To address this, we developed an in situ Complementomics platform enabling spatial mapping of complement components, fragments, and receptors alongside immune and structural markers, using hyperplexed immunofluorescence and computational analysis. After validating the approach in human tonsils, we applied it to kidney biopsies from patients with lupus nephritis (LN), a prototype immune complex disease; cholesterol crystal embolism–associated acute kidney injury (CCE-AKI), a vascular injury model with suspected complement involvement; and diabetic nephropathy (DN), used as a control. In LN, we identified a glomerular endotype marked by intense complement deposition and infiltration by C5aR1⁺ myeloid cells, associated with serologic and histologic disease activity and predictive of persistent proteinuria. In CCE-AKI, we uncovered robust complement activation within small renal arteries, involving classical and lectin pathways, accompanied by endothelial injury and dense perivascular infiltration by C5aR1⁺ macrophages correlating with systemic C5a elevation. These results prompted treatment of one patient with C5aR1 inhibition using avacopan, which led to reduced systemic inflammation and attenuated activation of blood myeloid cells, as evidenced by reduced CD11b expression and C5a-induced cytokine production. Together, our results demonstrate that in situ Complementomics enables identification of pathogenic complement–immune endotypes across diseases and may guide rational use of complement-targeted therapies.