Validation of non-destructive morphology-based selection of cerebral cortical organoids by paired morphological and single-cell RNA-seq analyses

• Published in: Stem cell reports 2024-11, Vol.19 (11), p.1635-1646
• Main Authors: Ikeda, Megumi, Doi, Daisuke, Ebise, Hayao, Ozaki, Yuki, Fujii, Misaki, Kikuchi, Tetsuhiro, Yoshida, Kenji, Takahashi, Jun
• Format: Article
• Language: English
• Subjects: Animals; Cell Differentiation - genetics; cell therapy; Cerebral Cortex - cytology; cerebral organoid; Choroid Plexus - cytology; heterogeneity; human pluripotent stem cell; Humans; Mice; morphology; Neural Crest - cytology; Neural Crest - metabolism; oraganoid differentiation; Organoids - cytology; Organoids - metabolism; regenerative medicine; Resource; RNA-Seq - methods; Sequence Analysis, RNA - methods; single cell RNA sequencing; Single-Cell Analysis - methods; Single-Cell Gene Expression Analysis
• ISSN: 2213-6711; 2213-6711
• DOI: 10.1016/j.stemcr.2024.09.005

Organoids, self-organized cell aggregates, contribute significantly to developing disease models and cell-based therapies. Organoid-to-organoid variations, however, are inevitable despite the use of the latest differentiation protocols. Here, we focused on the morphology of organoids formed in a cerebral organoid differentiation culture and assessed their cellular compositions by single-cell RNA sequencing analysis. The data revealed that organoids primarily composed of non-neuronal cells, such as those from the neural crest and choroid plexus, showed unique morphological features. Moreover, we demonstrate that non-destructive morphological analysis can accurately distinguish organoids composed of cerebral cortical tissues from other cerebral tissues, thus enhancing experimental accuracy and reliability to ensure the safety of cell-based therapies. [Display omitted] •Organoids in a cerebral differentiation culture could be classified by morphology•Cell types in organoids could be identified by morphology and scRNA-seq•Organizing signals were locally activated at the early stages of differentiation•Non-destructive morphological selection enabled the collection of desired organoids Ikeda et al. paired scRNA-seq and morphological analyses to identify the cellular composition of a heterogeneous collection of morphologically distinct organoids generated in cerebral organoid differentiation. This work illustrates the potential for the non-destructive morphological selection of target organoids to reduce tissue heterogeneity for research and improve the safety of cell-based therapies.