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Background <p>Glomerulonephritis (GN) comprises a heterogeneous group of immune-mediated kidney disorders with substantial biological and clinical diversity. Current treatment still relies largely on broad immunosuppression, underscoring the need for mechanism-informed target discovery across GN phenotypes.</p> Methods <p>We performed a program-guided integrative multi-omics study by combining cis-expression quantitative trait loci and cis-protein quantitative trait loci with GN genome-wide association datasets from UK Biobank, the GWAS Catalog, and FinnGen. Candidate genes were organized into four predefined mechanistic programs: cytokine/TNF signaling, cell-cycle/senescence–repair balance, complement/innate immune activation, and regulated cell-death/redox stress. Six GN-related outcomes were analyzed. Bayesian colocalization, cross-dataset meta-analysis, mouse knockout annotation, drug-repurposing assessment, network pharmacology, and rule-based evidence scoring were used to refine target prioritization.</p> Results <p>Integrative screening identified 42 transcriptomic and 12 proteomic putative targets, with the strongest enrichment in non-proliferative glomerulonephritis and primary membranoproliferative glomerulonephritis. Bayesian colocalization supported PPP2R1B in non-proliferative glomerulonephritis, SOD1 in IgA nephropathy, and CDK4 in primary membranoproliferative glomerulonephritis. Among 42 transcriptomic gene–outcome pairs taken forward, 11 were supported by cross-dataset meta-analysis. Proteomic meta-analysis supported several cross-dataset signals, including protective associations of ANXA5, GSR, and TNFRSF1B with glomerulonephritis. Across outcomes, complement/innate immunity and cytokine/TNF signaling formed the dominant shared backbone. After separating MHC-region signals for cautious interpretation, 31 non-MHC targets were retained for primary prioritization, with PPP2R1B, CDK4, and SOD1 comprising the top tier.</p> Conclusions <p>This mechanism-centered integrative multi-omics study delineates shared and phenotype-enriched biological programs across the GN spectrum and identifies a prioritized set of candidate targets for future validation and therapeutic development.</p>

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Mechanism-centered target discovery across glomerulonephritis phenotypes: an integrative multi-omics study

  • 期刊论文

  • 发表日期：

    2026年6月29日

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  • Jiachen Liu,
  • Xiaorui Qiu,
  • Dianjie Zeng,
  • Yue Li,
  • Yuxi Wang,
  • Jiashu Gu,
  • Yashpal S. Kanwar,
  • Leyi Chen,
  • Chenming Wei,
  • Yinhuai Wang,
  • Wenpeng Wang,
  • Liya Sun

摘要

Background

Glomerulonephritis (GN) comprises a heterogeneous group of immune-mediated kidney disorders with substantial biological and clinical diversity. Current treatment still relies largely on broad immunosuppression, underscoring the need for mechanism-informed target discovery across GN phenotypes.

Methods

We performed a program-guided integrative multi-omics study by combining cis-expression quantitative trait loci and cis-protein quantitative trait loci with GN genome-wide association datasets from UK Biobank, the GWAS Catalog, and FinnGen. Candidate genes were organized into four predefined mechanistic programs: cytokine/TNF signaling, cell-cycle/senescence–repair balance, complement/innate immune activation, and regulated cell-death/redox stress. Six GN-related outcomes were analyzed. Bayesian colocalization, cross-dataset meta-analysis, mouse knockout annotation, drug-repurposing assessment, network pharmacology, and rule-based evidence scoring were used to refine target prioritization.

Results

Integrative screening identified 42 transcriptomic and 12 proteomic putative targets, with the strongest enrichment in non-proliferative glomerulonephritis and primary membranoproliferative glomerulonephritis. Bayesian colocalization supported PPP2R1B in non-proliferative glomerulonephritis, SOD1 in IgA nephropathy, and CDK4 in primary membranoproliferative glomerulonephritis. Among 42 transcriptomic gene–outcome pairs taken forward, 11 were supported by cross-dataset meta-analysis. Proteomic meta-analysis supported several cross-dataset signals, including protective associations of ANXA5, GSR, and TNFRSF1B with glomerulonephritis. Across outcomes, complement/innate immunity and cytokine/TNF signaling formed the dominant shared backbone. After separating MHC-region signals for cautious interpretation, 31 non-MHC targets were retained for primary prioritization, with PPP2R1B, CDK4, and SOD1 comprising the top tier.

Conclusions

This mechanism-centered integrative multi-omics study delineates shared and phenotype-enriched biological programs across the GN spectrum and identifies a prioritized set of candidate targets for future validation and therapeutic development.