A Hybrid 2D‐to‐3D in vitro Differentiation Platform Improves Outcomes of Cerebral Cortical Organoid Generation in hiPSCs

Abstract Three‐dimensional (3D) cerebral cortical organoids are popular in vitro cellular model systems widely used to study human brain development and disease, compared to traditional stem cell–derived methods that use two‐dimensional (2D) monolayer cultures. Despite the advancements made in protocol development for cerebral cortical organoid derivation over the past decade, limitations due to biological, mechanistic, and technical variables remain in generating these complex 3D cellular systems. Building from our previously established differentiation system, we have made modifications to our existing 3D cerebral cortical organoid protocol that resolve several of these technical and biological challenges when working with diverse groups of human induced pluripotent stem cell (hiPSC) lines. This improved protocol blends a 2D monolayer culture format for the specification of neural stem cells and expansion of neuroepithelial progenitor cells with a 3D system for improved self‐aggregation and subsequent organoid development. Furthermore, this “hybrid” approach is amenable to both an accelerated cerebral cortical organoid protocol as well as an alternative long‐term differentiation protocol. In addition to establishing a hybrid technical format, this protocol also offers phenotypic and morphological characterization of stage‐specific cellular profiles using antibodies and fluorescent‐based dyes for live cell imaging. © 2024 Wiley Periodicals LLC. Basic Protocol 1 : hiPSC‐based 2D monolayer specification into neural stem cells (NSCs) Basic Protocol 2 : Serial passaging and 2D monolayer expansion of neuroepithelial progenitor cells (NPCs) Support Protocol 1 : Direct cryopreservation and rapid thawing of NSCs and NPCs Basic Protocol 3 : Bulk aggregation of 3D neurospheres and accelerated cerebral cortical organoid differentiation Alternate Protocol 1 : Bulk aggregation of 3D neurospheres and long‐term cerebral cortical organoid differentiation Support Protocol 2 : High‐throughput 3D neurosphere formation and 2D neurosphere migration assay Support Protocol 3 : LIVE/DEAD stain cell imaging assay of 3D neurospheres Support Protocol 4 : NeuroFluor NeuO live cell dye for 3D cerebral cortical organoids