Key Points

Calcineurin inhibition deactivated pyruvate dehydrogenase and induced proximal tubule cell metabolic dysfunction.The impaired mitochondrial metabolism caused a proinflammatory, profibrotic phenotype, thereby contributing to kidney fibrosis.Metabolic dysfunction in tubular cells is a potential target for intervention in chronic calcineurin inhibitor nephrotoxicity.

Background

Calcineurin inhibitors (CNIs) 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 CNI nephrotoxicity at single-cell resolution, kidney tissues from a chronic CNI 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 per day cyclosporin A, 3 mg/kg per 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 CNI 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, CNIs 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 CNI 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 CNI nephrotoxicity, appearing at an early stage.