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Understanding human organ formation is a scientific challenge with far-reaching medical implications1,2. Three-dimensional stem-cell cultures have provided insights into human cell differentiation3,4. However, current approaches use scaffold-free stem-cell aggregates, which develop non-reproducible tissue shapes and variable cell-fate patterns. This limits their capacity to recapitulate organ formation. Here we present a chip-based culture system that enables self-organization of micropatterned stem cells into precise three-dimensional cell-fate patterns and organ shapes. We use this system to recreate neural tube folding from human stem cells in a dish. Upon neural induction5,6, neural ectoderm folds into a millimetre-long neural tube covered with non-neural ectoderm. Folding occurs at 90% fidelity, and anatomically resembles the developing human neural tube. We find that neural and non-neural ectoderm are necessary and sufficient for folding morphogenesis. We identify two mechanisms drive folding: (1) apical contraction of neural ectoderm, and (2) basal adhesion mediated via extracellular matrix synthesis by non-neural ectoderm. Targeting these two mechanisms using drugs leads to morphological defects similar to neural tube defects. Finally, we show that neural tissue width determines neural tube shape, suggesting that morphology along the anterior–posterior axis depends on neural ectoderm geometry in addition to molecular gradients7. Our approach provides a new route to the study of human organ morphogenesis in health and disease. Stem cells cultured in a micropattern-constrained platform form a quantitative and robust model of human neural tube morphogenesis.

SummaryThe human embryo breaks symmetry to form the anterior-posterior axis of the body. As the embryo elongates along this axis, progenitors in the tailbud give rise to axial tissues that generate the spinal cord, skeleton, and musculature. The mechanisms underlying human axial elongation are unknown. While ethics necessitate in vitro studies, the variability of human organoid systems has hindered mechanistic insights. Here we developed a bioengineering and machine learning framework that optimizes symmetry breaking by tuning the spatial coupling between human pluripotent stem cell-derived organoids. This framework enabled the reproducible generation of hundreds of axially elongating organoids, each possessing a tailbud and an epithelial neural tube with a single lumen. We discovered that an excitable system composed of WNT and FGF signaling drives axial elongation through the induction of a signaling center in the form of neuromesodermal progenitor (NMP)-like cells. The ability of NMP-like cells to function as a signaling center and drive elongation is independent of their potency to generate mesodermal cell types. We further discovered that the instability of the underlying excitable system is suppressed by secreted WNT inhibitors of the secreted frizzled-related protein (SFRP) family. Absence of these inhibitors led to the formation of ectopic tailbuds and branches. Our results identify mechanisms governing stable human axial elongation to achieve robust morphogenesis.