Deciphering Brain Organoids Heterogeneity by Identifying Key Quality Determinants

Kachkin, D.; Zagha, N.; Boerstler, T.; Furlanetto, F.; Nayebzade, N.; Zappia, L.; Boisvert, M.; Farrell, M.; Ploetz, S.; Regensburger, M.; Guenther, C.; Winkler, J.; Gupta, P.; Theis, F.; Karow, M.; Falk, S.; Winner, B.; Krach, F.

doi:10.1101/2025.01.13.632763

bioRxiv · 10.1101/2025.01.13.632763

Deciphering Brain Organoids Heterogeneity by Identifying Key Quality Determinants

Kachkin, D.·Zagha, N.·Boerstler, T.·Furlanetto, F.·Nayebzade, N.·Zappia, L.·Boisvert, M.·Farrell, M.·Ploetz, S.·Regensburger, M.·Guenther, C.·Winkler, J.·Gupta, P.·Theis, F.·Karow, M.·Falk, S.·Winner, B.·Krach, F.

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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 further confirmed the reliability of this marker and identified a negative impact of mesenchymal cells on the abundance of organoid formation. High-quality organoids consistently displayed a lower mesenchymal cell presence. These findings offer a framework for enhancing brain organoid standardization and reproducibility, underscoring the need for morphological quality controls and the consideration of mesenchymal cell influence on organoid-based modeling. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/632763v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@11c214org.highwire.dtl.DTLVardef@1dcb643org.highwire.dtl.DTLVardef@1420141org.highwire.dtl.DTLVardef@6074e6_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Kachkin, D., Zagha, N., Boerstler, T., Furlanetto, F., Nayebzade, N., Zappia, L., Boisvert, M., Farrell, M., Ploetz, S., Regensburger, M., Guenther, C., Winkler, J., Gupta, P., Theis, F., Karow, M., Falk, S., Winner, B., Krach, F.. 2025-01-13. Deciphering Brain Organoids Heterogeneity by Identifying Key Quality Determinants. https://doi.org/10.1101/2025.01.13.632763

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