CD39+ Regulatory T Cells Mediate Renal Protection in Membranous Nephropathy: Integrated Mendelian Randomization and Multiomics Analysis

Background: Membranous nephropathy (MN) is an autoimmune glomerular disease characterized by B cell-mediated injury; however, the role of regulatory T cells (Tregs)—especially the CD39+ subset—remains unclear. We hypothesized that CD39+ Tregs protect against MN and may serve as promising diagnostic and therapeutic targets. Methods: We conducted an integrative analysis combining multi-omics data and Mendelian randomization (MR) to elucidate the role of CD39+ Tregs in MN. Public bulk transcriptomic data and scRNA-seq data were analyzed to characterize immune cell profiles in MN. A modular MR pipeline was developed to assess causal relationships between immune cell traits and MN. Advanced machine learning techniques refined a 11-gene CD39+ Treg signature model for MN diagnosis. Finally, molecular docking and molecular dynamics simulations were performed to screen FDA-approved drugs targeting ADA2, a key enzyme linked to increased CD39+ Treg levels and reduced MN risk. Results: Molecular profiling revealed increased Treg infiltration in MN renal tissue. MR established that genetically elevated CD39+ Treg proportions were causally associated with both reduced MN risk and improved renal prognostic indicators. Pathway analysis of CD39+ Tregs showed enrichment of survival and anti-inflammatory signaling. Genetically predicted ADA2 expression correlated positively with CD39+ Treg abundance and inversely with MN risk. Based on CD39+ Treg expression signatures, we developed and validated an 11-gene diagnostic model (AUC=0.78 in test set). Finally, virtual drug repositioning identified venetoclax as a promising ADA2-targeting candidate. Conclusion: CD39+ Tregs play a central protective role in MN pathogenesis and prognosis. Integration of CD39+ Treg related biomarkers support novel diagnostic tools, and repositioning venetoclax to modulate the ADA2-CD39+ Treg axis offers a potential precision-based immunotherapeutic strategy for MN management. Funding: Government Support – Non-U.S.Graphical abstract