Proteomic insights into the dynamic inflammatory and metabolic networks of renal ischemia-reperfusion injury.

Abstract

The molecular mechanisms underlying the transition from ischemia-reperfusion injury (IRI)-induced acute kidney injury (AKI) to chronic kidney disease (CKD) remain poorly defined. In this study, a murine IRI model was established by bilateral renal pedicle clamping. Kidney tissues harvested on postoperative day 2 (IRI-2d, acute phase) and day 28 (IRI-28d, chronic phase) were analyzed using 4D label-free quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 5351 proteins were identified, among which 910 and 329 were differentially expressed in the IRI-2d and IRI-28d groups, respectively, compared with sham controls. Enrichment analyses revealed consistent suppression of amino acid and lipid metabolic pathways during the acute phase, whereas inflammatory pathways, particularly complement and coagulation cascades, were robustly activated. By day 28, metabolic suppression persisted, while inflammatory activity had declined below baseline levels. Weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network analysis further demonstrated strong associations between metabolic pathways and the acute and chronic stages of IRI, highlighting glycine, serine and threonine metabolism pathways may be a key driver in these stages, and identified Sarcosine Dehydrogenase (Sardh), serine hydroxymethyltransferase 1 (Shmt1), and serine hydroxymethyltransferase 2 (Shmt2) as core hub proteins throughout the phase. Collectively, these findings delineate the dynamic proteomic landscape following renal IRI, underscore the divergent roles of metabolism and inflammation across disease stages, and provide a framework for developing stage-specific and precision kidney-protective strategies.