Fátima Sanchís-Calleja, Nadezhda V. Azbukina, Akanksha Jain, Zhisong He, Ryoko Okamoto, Charlotte Rusimbi, Pedro Rifes, Gaurav Singh Rathore, Małgorzata Santel, Jasper Janssens, Makiko Seimiya, Benedikt Eisinger, Jonas Simon Fleck, Agnete Kirkeby, J. Gray Camp, Barbara Treutlein
Morphogens direct neuroepithelial fates toward discrete regional identities in vivo. Neural organoids provide models for studying neural regionalization through morphogen exposure; however, we lack a comprehensive survey of how the developing human neuroepithelium responds to morphogen cues. Here we produce a detailed survey of morphogen-induced effects on the regional specification of human neural organoids using multiplexed single-cell transcriptomic screens. We find that the timing, concentration and combination of morphogens strongly influence organoid cell-type and regional composition, and that cell line and neural induction method impact the response to a given morphogen condition. We apply concentration gradients in microfluidic chips or increasing static concentrations in multi-well plates and observe different patterning dynamics in each scenario. Altogether, we provide a detailed resource on neural lineage specification that, in combination with deep learning models, can enable the prediction of differentiation outcomes in human stem-cell-based systems.