Cell Type-Specific Metabolic Reprogramming in CKD and AKI

Background: Cellular metabolism plays a critical role in regulating cellular functions and energy production, and its dysregulation can drive disease development and progression. Characterizing metabolic reprogramming in pathological conditions provides valuable insights into disease mechanism and enables development of targeted therapeutic strategies. In this study, we present a comprehensive cell-type-specific metabolic landscape of the human kidney in disease conditions including chronic kidney disease (CKD) and acute kidney injury (AKI). Methods: We used single-cell RNA-seq data from 456,437 human kidney cells available from Cellxgene as input to the constraint-based flux-balanced model, COMPASS. To improve computational efficiency, we reduced the data size by creating micro-pools within each “organ-tissue region-original cell type” condition. We then applied Wilcoxon test on the reaction scores computed by COMPASS. Using the reaction ranks, we developed new methods to calculate count matrices for reactions and inferred metabolite levels for downstream analysis. We generated spatial metabolomic data from a rat kidney for validation. Results: Loop of Henle epithelial cells (LHEC) in CKD showed upregulation of leukotriene F4/E4, and Leukotriene C4 carboxypeptidase and Gamma-glutamyltransferase activities, which are potent proinflammatory mediators and enzymes involved in inflammatory response. LHEC in AKI showed upregulation of leukotriene A4 and prostaglandin that may contribute to inflammation and excessive excretion of solutes; NAD(P) nucleosidase which can be associated with decreased levels of NAD(P); and guanine deaminase which is associated with xanthine and uric acid production contributing to oxidative stress. Collecting duct cells (CDC) in CKD showed upregulation of xylulose reductase activity that may reduce oxidative stress. Conversly, CDC showed upregulation of sphingosine phosphate lyase activity that can lead to reduced levels of sphingosine-1-phosphate, contributing to cellular injury. We compared tissue-specific metabolite profiles inferred by the flux model with spatial metabolomic data and observed 57% similarity in metabolite differences between kidney cortex and kidney medulla. Conclusion: In conclusion, CKD and AKI are associated with previously unrecognized metabolic changes in specific cell types including LHEC and CDC that may influence inflammation, oxidative stress, and cell survival. Funding: Other NIH Support - T32 HL007249-47; RC2 DK129964; P01 HL149620; R01 HL121233