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<p>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.</p><p></p>

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Deciphering brain organoid heterogeneity by identifying key quality determinants

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年10月1日

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  • Tom Boerstler,
  • Daniil Kachkin,
  • Elizaveta Gerasimova,
  • Naime Zagha,
  • Federica Furlanetto,
  • Negar Nayebzade,
  • Luke Zappia,
  • Michelle Boisvert,
  • Michaela Farrell,
  • Sonja Ploetz,
  • Iryna Prots,
  • Martin Regensburger,
  • Claudia Günther,
  • Juergen Winkler,
  • Pooja Gupta,
  • Fabian Theis,
  • Marisa Karow,
  • Sven Falk,
  • Beate Winner,
  • Florian Krach

摘要

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.