Pyruvate Dehydrogenase and Cellular Metabolism in Calcineurin Inhibitor–Induced Kidney Fibrosis

Background: Calcineurin inhibitors are indispensable immunosuppressants for transplant recipients and patients with autoimmune diseases, but chronic use causes nephrotoxicity, including kidney fibrosis. Why inhibiting calcineurin, a serine/threonine phosphatase, causes kidney fibrosis has not been fully elucidated. Methods: To characterize the phenotypic changes in the early stages of chronic calcineurin inhibitor nephrotoxicity at single-cell resolution, kidney tissues from a chronic calcineurin inhibitor nephrotoxicity mouse model and its control were subjected to single-nucleus RNA sequencing. ICR mice were fed a low-sodium diet and received 30 mg/kg/day cyclosporin A, 3 mg/kg/day tacrolimus or vehicle for up to 4 weeks. Primary human renal proximal tubule epithelial cells were cultured with cyclosporin A, tacrolimus or vehicle. Results: Single-nucleus RNA sequencing of the kidney from a chronic calcineurin inhibitor nephrotoxicity mouse model found a higher proportion of injured proximal tubule cells, which exhibited altered expression of genes associated with oxidative phosphorylation, cellular senescence and fibrosis. Analyses of publicly available transcriptomes of human kidneys confirmed that some of these manifestations were observed in human allograft kidneys under certain conditions. In cultured primary human renal proximal tubule epithelial cells, calcineurin inhibitors caused phosphorylation (deactivation) of pyruvate dehydrogenase, impaired mitochondrial metabolism, and senescence-associated phenotypes, all of which were ameliorated by pyruvate dehydrogenase activation. Finally, administration of dichloroacetic acid, a known activator of pyruvate dehydrogenase, in the chronic calcineurin inhibitor nephrotoxicity mouse model mitigated kidney fibrosis, increased the expression of genes that encode the electron transportation chain components, and decreased the expression of genes associated with proximal tubule injury, cellular senescence and fibrosis. Conclusions: Calcineurin inhibition deactivated pyruvate dehydrogenase and induced proximal tubule cell metabolic dysfunction, causing profibrotic phenotype. Metabolic dysfunction in proximal tubule cells may be a signature of chronic calcineurin inhibitor nephrotoxicity, appearing at an early stage.