Impaired Metabolic Remodeling Characterizes Injured Niches during Post-ischemic Kidney Repair

BACKGROUND: The role of the tissue microenvironment in the transition from acute kidney injury to chronic kidney disease remains poorly understood. While persistence of failed-repair proximal tubule cells is postulated to hamper kidney regeneration, the spatial metabolic architecture of injured tissue and its effect on regenerative capacity have not been fully characterized. METHODS: We analyzed mouse kidneys 14 days post bilateral ischemia-reperfusion injury using a multimodal spatial omics approach. Internal standard normalized mass spectrometry imaging (MSI) quantified metabolite abundances, followed by unsupervised spatial domain analysis using the BANKSY algorithm to identify tissue niches based on lipidome profiles. Consecutive sections underwent high-resolution spatial transcriptomics (Stereo-seq), and we applied niche projection to integrate metabolomic and transcriptomic data, enabling comparison of proximal tubule cells in healthy versus injured niches. RESULTS: Unsupervised spatial domain analysis revealed distinct healthy and injured niches, with injured niches exhibiting diffusely spread metabolic abnormalities extending beyond failed-repair proximal tubule cells. Quantitative metabolomics demonstrated that seemingly healthy proximal tubule cells residing in injured niches exhibited elevated succinic acid and depleted linoleic acid compared with cells in healthy niches. Spatial transcriptomics confirmed these metabolic defects at the transcriptional level, revealing downregulation of oxidative phosphorylation and fatty acid β-oxidation pathways in proximal tubule cells within injured microenvironments. CONCLUSIONS: Combined spatially resolved analysis of internal standard-normalized MSI and spatial transcriptomics revealed distinct healthy and injured tissue niches following ischemia-reperfusion injury. Metabolic abnormalities, including defects in oxidative phosphorylation and fatty acid β-oxidation, were not restricted to failed-repair proximal tubule cells but extended into seemingly healthy epithelial cells embedded within injured microenvironments.