A MULTIMODAL APPROACH TO UNDERSTANDING BRAIN ORGANOIDS MATURATION OVER TIME

The human brain exhibits complex developmental trajectories that are difficult to investigate due to the inaccessibility of living neural tissue. Human induced pluripotent stem cell (iPSC)-derived brain organoids provide a powerful in vitro platform to model early neurodevelopment, yet a comprehensive understanding of their maturation requires integrative, multimodal profiling.
In this study, we applied a multi-omic approach combining transcriptomics and metabolomics analyses, complemented by label‑free Raman imaging to characterize the temporal maturation of unguided iPSC-derived brain organoids. Transcriptome anlysis across multiple maturation times enabled inference of dynamic shifts in cell-type composition and gene expression programs associated with neurogenesis and regional specification. In parallel, Raman imaging provided a non-invasive biochemical fingerprint of organoid architecture, revealing changes in lipid, protein, and nucleic acid distributions during maturation. To complement these analyses, we performed untargeted metabolomic profiling to capture the evolving metabolic landscape of developing organoids, with a specific focus on pathways linked to neuronal energy metabolism, neurotransmitter and lipids biosynthesis.
By integrating these data layers, we generated a multi‑dimensional map of brain organoid development, uncovering coordinated molecular, metabolic, and structural transitions over time. This multi-ome framework establishes a benchmark for normal organoid maturation and offers a powerful strategy for the systematic characterization of patient-specific or disease-derived organoids, particularly for neurodevelopmental disorders lacking reliable animal models.