Minor glomerular abnormalities (MGAs) are a group of histopathologically heterogeneous renal lesions with subtle structural changes and latent clinical manifestations, accounting for a notable proportion of adult renal biopsies and associated with potential declines in renal function. Despite their clinical significance, the molecular mechanisms underlying MGAs remain poorly characterized, and there is a lack of specific biomarkers and evidence-based management protocols for this condition. Conventional proteomic analysis of renal biopsy samples is also challenged by limited tissue volume and low protein extraction efficiency, which restricts in-depth exploration of MGA’s molecular features.
Here, we employed a cutting-edge analytical workflow integrating PCT-assisted sample preparation with DIA mass spectrometry to systematically compare the proteomic profiles of distant non-neoplastic kidney tissues (n = 24) and MGA tissues (n = 27). This approach achieved efficient protein extraction from microscale renal samples and high-resolution proteomic quantification, with a total of 9,529 protein groups quantified at a false discovery rate <1%. We identified 1,338 differentially expressed protein groups (fold-change > 2 or < 0.5, P < 0.05) in MGA tissues, including 190 downregulated and 1,148 upregulated proteins.
Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed clear functional and pathway dysregulation in MGAs: downregulated proteins were enriched in cell adhesion, ion binding, and molecular transport, with metabolic pathways and the peroxisome proliferator-activated receptor signaling pathway inhibited; upregulated proteins clustered in transcriptional regulation, DNA replication/repair, and nucleic acid binding, accompanied by the activation of basal transcription factors and nucleotide excision repair pathways. Further screening identified 13 core upregulated nuclear proteins (e.g., YY1, TAF9, RFC1, POLR1D) with a detection rate >90% in MGA tissues, which are functionally associated with renal inflammation, cell proliferation, and the DNA damage response. Independent western blot validation confirmed the significant upregulation of key proteins (YY1, TAF9) in MGA tissues, verifying the reliability of our proteomic findings.
This work establishes the first comprehensive high-resolution proteomic landscape of MGAs, unraveling the core molecular alterations driving its pathogenesis and filling the gap in MGA tissue biomarker research. The 13 identified core nuclear proteins not only serve as potential diagnostic biomarkers but also represent promising therapeutic targets for MGAs, laying a foundation for the development of precise diagnostic methods and targeted interventions for this condition. Additionally, the PCT-assisted DIA workflow overcomes the technical bottlenecks of microscale renal tissue proteomics, providing a robust and efficient technical framework for future proteomic research on kidney diseases. The work entitled “Pressure cycling technology-assisted data-independent acquisition proteomics reveals molecular alterations and potential therapeutic targets in minor glomerular abnormalities” was published on Precision Clinical Medicine (published on Feb. 13, 2026).
DOI:10.1093/pcmedi/pbag006