• Patient-derived iPSC model of macular corneal dystrophy recapitulates disease-specific mitochondrial and autophagy impairments in corneal stromal keratocytes.
• Trehalose treatment restores autophagic flux and mitochondrial membrane potential, reducing protein aggregates in MCD-iCSKs.
• This study provides a human-relevant platform for mechanistic studies and drug screening for MCD.
• Trehalose emerges as a potential non-surgical therapeutic candidate for managing macular corneal dystrophy.
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