Retinal pigment epithelium (RPE) degeneration is a major cause of vision loss in multiple retinal diseases, including age-related macular degeneration, Bietti crystalline dystrophy and Stargardt disease. Induced pluripotent stem cell (iPSC)-derived RPE cells hold promise for regenerative therapies. B27- and KSR-based media are among the most commonly used for RPE culture; however, how these culture conditions shape RPE cell identity and features remain incompletely understood. Here, we performed comprehensive transcriptomic and metabolomic profiling of iPSC-derived RPE cells cultured in B27 or KSR media to systematically compare their gene expression and metabolic features. B27- and KSR-cultured RPE cells exhibited distinct morphologies and barrier properties. Integrated multi-omics analyses revealed that KSR-cultured RPE cells displayed a relative bias toward fatty acid oxidation and oxidative phosphorylation, whereas B27-cultured RPE cells showed a relative bias toward glycolytic metabolism. The glycolytic tendency observed in B27-RPE cells was accompanied by increased expression of extracellular matrix–related genes and higher transepithelial resistance. In contrast, KSR-RPE cells exhibited comparable tricarboxylic acid cycle activity but higher expression of oxidative phosphorylation–related genes compared with B27-RPE cells. Together, these results demonstrate that RPE cells cultured under different conditions adopt distinct but partially overlapping metabolic and transcriptional states, which are associated with differences in RPE-related features and barrier properties. Our findings highlight the importance of metabolic balance between glycolysis and fatty acid oxidation in shaping in vitro RPE phenotypes.
Zhang et al. (Fri,) studied this question.