Here we report a microfluidics method to enrich physically deformable cells by mechanical manipulation through artificial microbarriers. Driven by hydrodynamic forces, flexible cells or cells with high metastatic propensity change shape to pass through the microbarriers and exit the separation device, whereas stiff cells remain trapped. We demonstrate the separation of (i) a mixture of two breast cancer cell types (MDA-MB-436 and MCF-7) with distinct deformabilities and metastatic potentials, and (ii) a heterogeneous breast cancer cell line (SUM149), into enriched flexible and stiff subpopulations. We show that the flexible phenotype is associated with overexpression of multiple genes involved in cancer cell motility and metastasis, and greater mammosphere formation efficiency. Our observations support the relationship between tumor-initiating capacity and cell deformability, and demonstrate that tumor-initiating cells are less differentiated in terms of cell biomechanics.cell mechanics | cytoskeleton | genomic profiling C ell deformability is commonly measured using magnetic twisting cytometry, particle tracking rheometry, optical tweezers, micropipette aspiration, atomic force microscope, and other derivative cell stretching or poking methods (1-4). Applications of these methods to stem cells have revealed the greater deformability of the cytoskeleton and nucleoskeleton in less differentiated cells, whereby deformability generally decreases during differentiation to mature cells (5-8). Research on cancer cell deformability has also consistently revealed that increased deformability is correlated with increased metastatic potential (9-15).Despite the success achieved using cell deformability measurements, isolation of cells with differential deformabilities remains a great challenge (10, 16). Microfabrication-assisted technology, using microscale arrays of round or rectangular posts, channels, or other simple patterns, has the potential to solve this problem (17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27). Here, we focused on the mechanical properties of cancer cells in designing a unique cell purification system for the purpose of generating subpopulations enriched in highly deformable cells. We used microfabrication technology and obtained a subpopulation of SUM149 breast cancer cells with stem-cell-like deformability and mammosphere formation capability.The separation device, a mechanical separation chip (MS-chip), employs artificial microbarriers in combination with hydrodynamic force to separate deformable from stiff cells (Fig. 1A). Both the microbarrier structures and the fluidic parameters are essential to the cell-enrichment process. The most notable feature of the device is the precise placement of the microbarriers to impede the passage of stiff cells. Published in vivo observations suggest that the minimum crossable barrier for cancer cells is ∼8 μm or less (28,29). Here, we took those barrier dimensions into account in designing the MSchip to separate cells based on perfusion through constrictions. As...