Metabolic profiling of retinal organoids reveals conserved core metabolites and alterations in glycolytic, and amino acid pathways

Abstract Introduction: Retinal organoids have emerged as powerful models of retinal development and disease; however, the extent to which they recapitulate the metabolic landscape of the native retina remains largely unknown. Objectives This study aimed to compare the metabolomic profiles of mouse retina and mouse embryonic stem cell-derived retinal organoids and to evaluate metabolic changes during organoid maturation. Methods Untargeted gas chromatography mass spectrometry (GCMS) based metabolomic profiling was performed on intracellular metabolites from mouse retina and mouse retinal organoids (MRO), together with media collected during organoid maturation. Statistical, visualization and pathway enrichment analyses were performed. Results A total of 166 metabolites were detected in both mouse retina and MRO. 29 were significantly altered, while 15 metabolites were detected only in mouse retina and 3 in retinal organoids. Retinal organoids have emerged as powerful models of retinal development and disease; however, the extent to which they recapitulate the metabolic landscape of the native retina remains largely unknown. preserved a substantial conserved retinal metabolic signature but demonstrated selective divergence in glycolysis-associated metabolites and pentose phosphate pathway intermediates including glucose-6-phosphate and ribulose-5-phosphate, as well as tricarboxylic acid-cycle-associated (TCA) metabolites including citric acid, fumaric acid and oxalic acid. Pathway analysis identified significant alterations in alanine, aspartate, and glutamate metabolism. Media analysis further revealed stage-dependent increases in extracellular glutamate and glycine abundance during organoid maturation. Conclusion MRO retain major components of retinal metabolic organization while exhibiting features suggestive of incomplete metabolic maturation compared with native retina. These findings provide valuable insight into MRO metabolic fidelity and guide future optimization strategies.