The role of lysosomal cystine in development of the phenotype in cystinosis is problematic, in that the cystine is effectively isolated from the rest of cellular metabolism. Several models have been proposed, but most do not provide a mechanism for such an interaction. During early apoptosis the lysosomes are permeablized, providing such access. We have shown that lysosomal cystine enhances apoptosis in cultured normal and cystinotic fibroblasts and cultured renal proximal tubule epithelial cells, that the process occurs via mixed disulfide (cysteinylation) formation, and that PKC delta is involved. Further, the "swan neck" deformity of proximal renal tubules, long a hallmark of cystinosis, is explicable via this model, as is the renal failure that results from progression of tubule cell loss to atubular glomeruli. Modification of this process by other genes may explain the milder forms of the disease.