A phenotypic brain organoid atlas for neurodevelopmental disorders

Wang, L.; Nakamura, Y.; Li, J.; Sievert, D.; Liu, Y.; Nguyen, T.; Jetti, P. S.; Thai, E.; Zhou, R. Y.; Weng, J.; Meave, N.; Yadavilli, M.; Howarth, R.; Camey, K.; Banka, N.; Owusu-Hammond, C.; Barrows, C.; Kingsmore, S. F.; Zaki, M. S.; Mukamel, E. A.; Gleeson, J. G.

doi:10.1101/2025.09.12.675864

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bioRxiv · 10.1101/2025.09.12.675864

A phenotypic brain organoid atlas for neurodevelopmental disorders

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Abstract

Thousands of genes are associated with neurodevelopmental disorders (NDDs), yet mechanisms and targeted treatments remain elusive. To fill these gaps, we present a CIRM-initiated NDD biobank of 352 publicly-available genetically-diverse patient-derived iPSCs, along with clinical details, brain imaging and genomic data, representing four major categories of disease: microcephaly (MIC), polymicrogyria (PMG), epilepsy (EPI), and intellectual disability (ID). From 35 representative patients, we studied over 6000 brain organoids for histology and single cell transcriptomics. Compared with an organoid library from ten neurotypicals, patients showed distinct cellular defects linked to underlying clinical disease categories. MIC showed defects in cell survival and excessive TTR+ cells, PMG showed intermediate progenitor cell junction defects, EPI showed excessive astrogliosis, and ID showed excessive generation of TTR+ cells. Our organoid atlas demonstrates both conserved and divergent NDD category-specific phenotypes, bridging genotype and phenotype. This NDD iPSC biobank can support future disease modeling and therapeutic approaches. HIGHLIGHTSO_LIResource of 352 CIRM-funded genetically-diverse IPSC lines from patients with neurodevelopmental disorders (NDDs). C_LIO_LIGenome/exome and brain images available for these genetically-diverse IPSC lines. C_LIO_LIDerived human brain organoids (hBOs) show disease-specific histological and cellular phenotypes. C_LIO_LIhBO phenotypes show unanticipated differentiation towards non-neuronal cell fates in NDDs. C_LI

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Wang, L., Nakamura, Y., Li, J., Sievert, D., Liu, Y., Nguyen, T., Jetti, P. S., Thai, E., Zhou, R. Y., Weng, J., Meave, N., Yadavilli, M., Howarth, R., Camey, K., Banka, N., Owusu-Hammond, C., Barrows, C., Kingsmore, S. F., Zaki, M. S., Mukamel, E. A., Gleeson, J. G.. 2025-09-13. A phenotypic brain organoid atlas for neurodevelopmental disorders. https://doi.org/10.1101/2025.09.12.675864

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