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

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 based metabolomic profiling was performed on intracellular metabolites from mouse retina at postnatal day 3 and mouse retinal organoids (MROs) at differentiation day 28, together with conditioned media collected during organoid maturation. RESULTS: Across mouse retina and retinal organoids, 166 annotated compounds were included in the analysis . Of these, 148 were shared between the two sample types. Using a bidirectional fold-change threshold, differential analysis showed that mouse retinal organoids preserved a substantial metabolic signature shared with mouse retina. However, selective differences were observed in the abundance of glycolysis-associated metabolites and pentose phosphate intermediates including glucose-6-phosphate and ribulose-5-phosphate, as well as tricarboxylic acid-cycle-associated metabolites including citric acid, fumaric acid and oxalic acid. Pathway enrichment analysis identified significant alterations in alanine, aspartate, and glutamate metabolism. Media analysis further revealed stage-dependent changes in extracellular glutamate and glycine abundance during organoid maturation. CONCLUSION: MRO retains 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.