Cultured rat primitive extraembryonic endoderm (pXEN) cells easily form free-floating multicellular vesicles de novo, exemplifying a poorly studied type of morphogenesis. Here, we reveal the underlying mechanism and the identity of the vesicles. We resolve the morphogenesis into vacuolization, vesiculation, and maturation, and define molecular characteristics and requirements of each step. Vacuolization is triggered by reducing both matrix proteins and cell-cell contact, and driven by macropinocytosis. Fine-tuned cell-cell contact then forms nascent 3-cell vesicles with vacuole-derived lumina. In maturation, the vesicles complete epithelialization, expand via mitosis and continued fluid uptake, and differentiate further. The mature vesicles consist of a simple, squamous epithelium with an apical-outside/basal-inside polarity that we trace back to the single-cell stage. The polarity and gene expression pattern of the vesicles are similar to the early visceral endoderm. pXEN cells provide a useful in vitro model for studying matrix-independent, basal-type lumenogenesis and the physiology of the visceral endoderm.

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