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Updated: May 6, 2026
Analyses of Proteinuria, Renal Infiltration of Leukocytes, and Renal Deposition of Proteins in Lupus-prone MRL/lpr Mice
Published on: June 8, 2022
Single-Cell Ligand-Receptor Profiling Identifies Targetable Signaling Axes and Therapeutic Candidates in Lupus
Introduction:
Ligand-receptor (LR) signaling shapes immune dynamics and tumor behavior in nephrotic kidney disease. However, LR-based subtype classification and therapeutic prediction remain underexplored.
Methods:
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.
Results:
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.
Discussion:
LR-driven epithelial-immune crosstalk centered on TGFBR2/TNFSF12 appears to define biologically distinct subtypes and yields repurposable candidates.
Conclusion:
Integrative analysis of LR crosstalk, knockdown experiments, and molecular docking reveals potential drug targets.
Insights
Ligand-receptor signaling in kidney disease defines subtypes and identifies TGFBR2/TNFSF12 as key targets. This research offers potential new therapeutic strategies for nephrotic kidney disease.
Area of Science:
- Immunology
- Molecular Biology
- Bioinformatics
Background:
- Ligand-receptor (LR) signaling is crucial for immune cell dynamics and tumor progression in nephrotic kidney disease.
- Current understanding of LR-based subtyping and therapeutic prediction in this context is limited.
Purpose of the Study:
- To classify nephrotic kidney disease subtypes using LR signaling.
- To identify potential therapeutic targets and repurposable drugs.
Main Methods:
- Single-cell RNA sequencing (scRNA-seq) data integration with Seurat.
- Intercellular signaling modeling using CellChat.
- Consensus clustering to stratify samples based on LR pairs.
- Gene Set Enrichment Analysis (GSEA) and Gene Ontology (GO) enrichment for functional evaluation.
- Immune infiltration profiling with CIBERSORT.
- Molecular docking and molecular dynamics (MD) simulations for ligand-target interactions.
- Knockdown experiments (siRNA) targeting TGFBR2 and TNFSF12.
- Validation assays including RT-qPCR, Western blotting, proliferation, colony formation, and wound-healing assays.
Main Results:
- Identification of eight distinct cell types, including inflammatory macrophages and fibroblasts.
- CellChat analysis revealed significant bidirectional signaling between epithelial and immune cells.
- Two major subtypes were identified: Clust1 with downregulated proliferation pathways and Clust2 with elevated plasma cells, Tregs, and CD8+ T cells.
- Knockdown of TGFBR2 and TNFSF12 impaired cell proliferation, colony formation, and wound closure.
- Mebendazole, progesterone, and demeclocycline were prioritized as potential drug candidates.
- Molecular docking and MD simulations confirmed stable binding affinities and conformations for prioritized ligands.
Conclusions:
- LR-driven crosstalk, particularly involving TGFBR2/TNFSF12, defines distinct nephrotic kidney disease subtypes.
- This study identifies potential drug targets and repurposable candidates for therapeutic intervention.
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