PCT-Assisted DIA Proteomics Reveals Molecular Alterations and Potential Therapeutic Targets in Minor Glomerular Abnormalities

Background Minor glomerular abnormalities (MGAs) are histopathologically heterogeneous renal lesions with subtle structural changes and latent clinical manifestations, yet their molecular mechanisms remain poorly characterized and underexplored. Methods In this study, we employed PCT-assisted sample preparation combined with DIA-MS to systematically compare the proteomic profiles of distant non-neoplastic tissues (DNTs, n = 24) and MGA tissues (n = 27). Results A total of 9,529 protein groups were quantified with a FDR < 1%, and 1,338 differentially expressed protein groups were identified (FC > 2 or < 0.5, P < 0.05), including 190 downregulated and 1,148 upregulated PGs in MGA tissues. GO analysis revealed that the downregulated proteins were enriched in cell adhesion, ion binding, and molecular transport, whereas the upregulated proteins were enriched in transcriptional regulation, DNA replication/repair, and nucleic acid binding. KEGG pathway analysis indicated that inhibition of metabolic pathways and PPAR signaling pathway, as well as the activation of basal transcription factors and nucleotide excision repair in MGAs. Further screening revealed 13 core upregulated nuclear proteins (e.g., YY1, TAF9, RFC1, and POLR1D) with an over 90% detection rate in MGA tissues; these proteins are functionally associated with renal inflammation, cell proliferation, and the DNA damage response. Conclusion Our study establishes a high-resolution proteomic landscape of MGAs, provides novel insights into their molecular pathogenesis, and identifies potential tissue biomarkers and therapeutic targets. The PCT-assisted DIA workflow also offers a robust technical framework for proteomic analysis of microscale renal biopsy samples.