Stage-specific and persistent transcriptomic and metabolomic alterations during unilateral ureteral obstruction in rats.

ObjectiveTo characterize time-dependent histopathological changes and identify stage-specific and persistent transcriptomic-metabolomic patterns in rat kidneys following unilateral ureteral obstruction (UUO).MethodsTwenty-three male Sprague-Dawley rats were assigned to a Sham group (n = 3) and four UUO groups (n = 5 per group), and kidney specimens were collected at 3, 7, 14 and 28 days after ureteral ligation. All 23 specimens were included in the final histological, transcriptomic and metabolomic analyses after specimen-level quality control. Kidney injury and fibrosis were assessed by hematoxylin and eosin and Masson's trichrome staining. RNA sequencing and LC-MS metabolomics were used to identify time-point-specific changes. Strict same-direction intersections defined persistent differentially expressed genes and metabolites. Persistent gene sets were analyzed by GO and KEGG over-representation analysis, followed by pathway-level integration based on KEGG annotations.ResultsHistological injury and fibrosis increased progressively after UUO. Across days 3, 7, 14 and 28, 219 genes were persistently upregulated and 335 were persistently downregulated. The upregulated set was enriched in immune, inflammatory and proliferative processes, whereas the downregulated set was enriched in transmembrane and ion transport. Metabolomic analysis identified 7 persistently increased and 51 persistently decreased metabolites. Integrated pathway analysis highlighted sustained changes in transport, oxidative phosphorylation, amino acid metabolism and purine metabolism.ConclusionUUO was accompanied by progressive histological injury and distinct stage-dependent and persistent molecular changes. The integrated analysis provides a temporal framework and identifies persistent pathways and molecular features for further investigation.