A Microfluidic Perfusion Culture Setup to Investigate Cell Migration in 3D Constrictions

Abstract Cell migration is a fundamental process underlying the morphological maturation of organs, but also in disease‐related conditions such as cancer. Cells are able to migrate through crowded space and a tight extracellular matrix (ECM). Passing through a constriction, a cell deforms strongly, including its nucleus. Such nuclear deformation can lead to changes in the 3D‐genomic architecture, and putatively, DNA methylation. However, the specific effects of deformation on cells are not well understood. It is highly desired to establish an ex vivo methodology to induce well‐defined cell deformation in complex geometrical constrictions. This study introduces a microfluidic system for the study of migrating cells in precisely controlled geometrical confinement. A procedure for coating, seeding of cerebellar granule cells, and perfusion culture is presented. By leveraging direct laser writing, channels with smooth, anisotropically curved surfaces on the cell‐scale can be fabricated. The system consists of constriction channels with a radius of 2 or 4 µm for the cells to pass through. This corresponds to a compression of the nucleus to 3.5% and 14.2% of its undeformed cross‐sectional area, respectively. The system can be used to investigate the influence of confinement geometry on the migration behavior and transcriptome of various cell types.