Systematic scRNA-seq screens profile neural organoid response to morphogens.

Area of Science:

• Neuroscience
• Developmental Biology
• Stem Cell Biology

Background:

• Morphogens are crucial for directing cell fates during embryonic development.
• Neural organoids offer a model to study human neurodevelopment in vitro.
• A comprehensive understanding of human neuroepithelial responses to morphogens is lacking.

Purpose of the Study:

• To comprehensively survey morphogen-induced regional specification in human neural organoids.
• To investigate how morphogen timing, concentration, and combinations affect neural cell-type and regional composition.
• To compare patterning dynamics under different morphogen application methods (microfluidics vs. multi-well plates).

Main Methods:

• Multiplexed single-cell transcriptomic screening of human neural organoids.
• Application of morphogen concentration gradients using microfluidic chips.
• Application of increasing static morphogen concentrations in multi-well plates.
• Analysis of cell-type and regional composition based on transcriptomic data.

Main Results:

• Morphogen timing, concentration, and combinations significantly influence organoid cell-type and regional identity.
• The response to morphogens is dependent on the specific cell line and neural induction method used.
• Different morphogen application methods (e.g., gradients vs. static concentrations) lead to distinct patterning dynamics.
• A detailed resource of morphogen-induced neural lineage specification was generated.

Conclusions:

• This study provides a detailed resource for understanding human neural lineage specification.
• The findings enable prediction of differentiation outcomes in human stem-cell-based systems when combined with deep learning models.
• This work advances the use of neural organoids for studying developmental neurobiology and disease modeling.