Proteomic Characterization of Replication Stress and Impaired Antioxidant Defense in Tacrolimus-Induced Chronic Nephrotoxicity

Tacrolimus (TAC) nephropathy is a major complication of immunosuppressive therapy and contributes to chronic kidney disease (CKD) progression through ischemia, metabolic dysfunction, and oxidative stress; however, its protein-level basis remains unclear. This study sought to identify characteristic molecular alterations in renal cortices of TAC-treated mice, so as to clarify the link between replication stress responses and metabolic dysfunction. A previously generated proteomic dataset from a TAC-induced chronic nephrotoxicity mouse model was analyzed using a protein-centered analytical strategy, including statistical, Gene Ontology, pathway, upstream regulator, and disease-enrichment analyses. A total of 7466 proteins were quantified. Upregulated proteins included KAT6A and NCKAP1, whereas downregulated proteins included NDUFC2, HSD17B12, and TECR. Coordinated impairment of CoQ10-dependent and glutathione-dependent antioxidant defenses was identified, reflected by reductions in AIFM2 (FSP1) and GSTA4/GSTT2. Enrichment analyses indicated activation of MCM- and ATR-associated replication stress responses in the upregulated group, and impaired lipid metabolism, CoA biosynthesis, mitochondrial function, and redox regulation in the downregulated group. TAC nephropathy is characterized by two major molecular signatures: central disruption of antioxidant defense systems, spanning FSP1-mediated CoQ10 regeneration and GST- associated antioxidant systems, together with suppression of lipid and energy metabolism and activation of replication stress responses. These findings provide a protein-level molecular framework linking coordinated impairment of antioxidant defense systems, suppression of lipid and energy metabolism, and activation of replication stress responses in TAC-induced chronic nephrotoxicity. These findings also suggest the FSP1 pathway, GST-associated antioxidant systems, and CoA-dependent metabolism as potential therapeutic targets for CKD progression.