Use of Human Induced Pluripotent Stem Cells and Kidney Organoids To Develop a Cysteamine/mTOR Inhibition Combination Therapy for Cystinosis

Significance Statement In its severest form, the lysosomal storage disease cystinosis is characterized by accumulation of cystine; renal proximal tubule dysfunction; and kidney failure. Research has also implicated cystinosin in modulating the mammalian target of rapamycin (mTOR) complex 1 pathway. Use of the cystine-depleting drug cysteamine, the sole treatment option for cystinosis, only slows disease progression. The authors developed induced pluripotent stem cell and kidney organoid models of cystinosis that exhibit elevated cystine levels, enlarged lysosomes, increased apoptosis, and defective basal autophagy. Although the latter is not rescued by cysteamine treatment, mTOR inhibition with everolimus was able to restore basal autophagy to levels of healthy controls. Dual treatment of everolimus and cysteamine rescued all of the observed cystinotic phenotypes in the models, suggesting that a combination therapy may improve outcomes in patients with cystinosis. Background Mutations in CTNS —a gene encoding the cystine transporter cystinosin—cause the rare, autosomal, recessive, lysosomal-storage disease cystinosis. Research has also implicated cystinosin in modulating the mTORC1 pathway, which serves as a core regulator of cellular metabolism, proliferation, survival, and autophagy. In its severest form, cystinosis is characterized by cystine accumulation, renal proximal tubule dysfunction, and kidney failure. Because treatment with the cystine-depleting drug cysteamine only slows disease progression, there is an urgent need for better treatments. Methods To address a lack of good human-based cell culture models for studying cystinosis, we generated the first human induced pluripotent stem cell (iPSC) and kidney organoid models of the disorder. We used a variety of techniques to examine hallmarks of cystinosis—including cystine accumulation, lysosome size, the autophagy pathway, and apoptosis—and performed RNA sequencing on isogenic lines to identify differentially expressed genes in the cystinosis models compared with controls. Results Compared with controls, these cystinosis models exhibit elevated cystine levels, increased apoptosis, and defective basal autophagy. Cysteamine treatment ameliorates this phenotype, except for abnormalities in apoptosis and basal autophagy. We found that treatment with everolimus, an inhibitor of the mTOR pathway, reduces the number of large lysosomes, decreases apoptosis, and activates autophagy, but it does not rescue the defect in cystine loading. However, dual treatment of cystinotic iPSCs or kidney organoids with cysteamine and everolimus corrects all of the observed phenotypic abnormalities. Conclusions These observations suggest that combination therapy with a cystine-depleting drug such as cysteamine and an mTOR pathway inhibitor such as everolimus has potential to improve treatment of cystinosis.