Deciphering brain organoids heterogeneity by identifying key quality determinants
Brain organoids derived from human pluripotent stem cells (hPSCs) hold immense potential for modeling neurodevelopmental processes and disorders. However, their experimental variability and undefined organoid selection criteria for analysis hinder reproducibility. As part of the Bavarian ForInter consortium, we generated 72 brain organoids from distinct hPSC lines. We conducted a comprehensive analysis of their morphological and cellular characteristics at an early stage of their development. In our assessment, the Feret diameter emerged as a reliable, single parameter that characterizes brain organoid quality. Transcriptomic analysis of our organoid identified the abundance of unintended mesodermal differentiation as a major confounder of unguided brain organoid differentiation, correlating with Feret diameter. High-quality organoids consistently displayed a lower presence of mesenchymal cells. These findings provide a framework for enhancing brain organoid standardization and reproducibility, underscoring the need for morphological quality controls and considering the influence of mesenchymal cells on organoid-based modeling.
Citation
@article{boerstler2025,
author = {Boerstler, Tom and Kachkin, Daniil and Gerasimova, Elizaveta
and Zagha, Naime and Furlanetto, Federica and Nayebzade, Negar and
Zappia, Luke and Boisvert, Michelle and Farrell, Michaela and
Ploetz, Sonja and Prots, Iryna and Regensburger, Martin and Günther,
Claudia and Winkler, Juergen and Gupta, Pooja and Theis, Fabian and
Karow, Marisa and Falk, Sven and Winner, Beate and Krach, Florian},
title = {Deciphering Brain Organoids Heterogeneity by Identifying Key
Quality Determinants},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1412},
date = {2025-10-01},
url = {https://doi.org/10.1038/s42003-025-08855-6},
doi = {10.1038/s42003-025-08855-6},
issn = {2399-3642},
langid = {en},
abstract = {Brain organoids derived from human pluripotent stem cells
(hPSCs) hold immense potential for modeling neurodevelopmental
processes and disorders. However, their experimental variability and
undefined organoid selection criteria for analysis hinder
reproducibility. As part of the Bavarian ForInter consortium, we
generated 72 brain organoids from distinct hPSC lines. We conducted
a comprehensive analysis of their morphological and cellular
characteristics at an early stage of their development. In our
assessment, the Feret diameter emerged as a reliable, single
parameter that characterizes brain organoid quality. Transcriptomic
analysis of our organoid identified the abundance of unintended
mesodermal differentiation as a major confounder of unguided brain
organoid differentiation, correlating with Feret diameter.
High-quality organoids consistently displayed a lower presence of
mesenchymal cells. These findings provide a framework for enhancing
brain organoid standardization and reproducibility, underscoring the
need for morphological quality controls and considering the
influence of mesenchymal cells on organoid-based modeling.}
}