A human induced pluripotent stem cell model for the holistic study of epithelial-to-mesenchymal transitions

The epithelial-to-mesenchymal transition (EMT) is a widely studied cell state change, yet differences in model design and measurement approaches limit comparison across studies. Addressing this challenge requires experimental model systems and analysis frameworks that support standardization across contexts. Here, we show that human induced pluripotent stem (hiPS) cells in defined cell culture geometries, two-dimensional colonies and three-dimensional lumenoids, enable multimodal measurements of EMT dynamics within a single experimental platform. Using fixed-cell and live-cell image-based assays, we quantify changes in cell migration, EMT-related molecular markers, cell–cell junction organization and interactions with the basement membrane, a specialized form of the extracellular matrix, during EMT induced in hiPS cells. We identify cell culture geometry-dependent differences in the timing of migration onset and show that basement membrane integrity can be quantitatively linked to these differences. Together, these results establish an imaging-based framework for analysis of cell state transitions and provide accessible datasets and tools.