Single-Cell Ligand-Receptor Profiling Identifies Targetable Signaling Axes and Therapeutic Candidates in Lupus Nephritis.

Ligand-receptor (LR) signaling shapes immune dynamics and tumor behavior in nephrotic kidney disease. However, LR-based subtype classification and therapeutic prediction remain underexplored. ScRNA-seq data were integrated using Seurat, and intercellular signaling was modeled using CellChat. Consensus clustering based on 65 highly correlated LR pairs (r > 0.4, p < 0.01) stratified samples into two subtypes. Functional differences were evaluated using GSEA and GO enrichment. Immune infiltration was profiled via CIBERSORT. Predicted ligands were subjected to molecular docking and 100 ns molecular dynamics simulations. To validate the roles of TGFBR2 and TNFSF12, knockdown experiments were performed in HK-2 and HEK293 cell lines using siRNA targeting TGFBR2 and TNFSF12. RT-qPCR, Western blotting, cell proliferation, colony formation, and wound-healing assays were used to validate the effects of the knockdown on cellular processes. Eight transcriptionally distinct cell types were identified, including inflammatory macrophages and fibroblasts. CellChat revealed strong bidirectional signaling among epithelial and immune cells. Consensus clustering identified two major subtypes, among which Clust1 showed downregulation of proliferation-associated Hallmark pathways, while Clust2 showed elevated plasma cells, Tregs, and CD8⁺ T cells. TGFBR2 and TNFSF12 knockdown significantly impaired cell proliferation and colony formation, and delayed wound closure compared to control groups. Mebendazole, progesterone, and demeclocycline were prioritized as drug candidates. Docking revealed strong binding affinities, and MD simulations confirmed stability with compact conformations and stable RMSD/Rg. LR-driven epithelial-immune crosstalk centered on TGFBR2/TNFSF12 appears to define biologically distinct subtypes and yields repurposable candidates. Integrative analysis of LR crosstalk, knockdown experiments, and molecular docking reveals potential drug targets.