Abstract / Summary
Background: Metabolic reprogramming and mitochondrial dysfunction are central features of acute kidney injury (AKI), yet their temporal relationship with proximal tubular cell-state remodeling remains incompletely understood. This study aimed to characterize early metabolic alterations and proximal tubular cell-state changes following ischemia–reperfusion injury (IRI). Methods: We integrated temporal single-nucleus RNA sequencing with complementary animal and cell-based experiments. The GSE139107 dataset comprised 79,526 kidney nuclei from 12 biological samples collected at Sham, 4 h, 12 h, and 2 d, including 34,151 proximal tubular nuclei. Analyses included subclustering, sample-level pseudobulk analysis, functional gene-set scoring, trajectory inference, and cell–cell communication analysis. Experimental validation was performed using a male mouse IRI model at 24 h of reperfusion and a tubular epithelial cell hypoxia–reoxygenation model. Results: Proximal tubular subclustering identified mature and segment-specific populations alongside stressed, injury-associated, repair-associated, and cycling states. Fatty acid oxidation, oxidative phosphorylation, and tubular transport programs were most strongly suppressed at 12 h, accompanied by reduced Ppara, Cpt1a, Sdhb, and Slc34a1 expression and increased injury-associated gene expression. Partial recovery of metabolic and transport programs occurred at 2 d, although cellular heterogeneity persisted. Monocle3 and Slingshot inferred transitions from mature proximal tubular cells toward stress-, repair-, cycling-, and injury-associated states, accompanied by declining metabolic and transport signatures. CellChat predicted remodeling of extracellular-matrix, adhesion, growth-factor, and guidance-related signaling. In male mice, IRI reduced PPARα, CPT1A, ATP5A, SDHB, and SLC34A1 levels while increasing KIM-1 and NGAL. Hypoxia–reoxygenation similarly decreased PPARα and CPT1A and increased cleaved caspase-3 in tubular epithelial cells. Conclusions: These findings reveal a temporally coordinated association among PPARα/CPT1A-related metabolic reprogramming, mitochondrial impairment, and proximal tubular cell-state remodeling during early ischemic AKI, highlighting the dynamic relationship between metabolic dysfunction and tubular injury responses.