Cancer cell sedimentation in 3D cultures reveals active migration regulated by self-generated gradients and adhesion sites

Cell sedimentation in 3D culture environments refers to the vertical migration of cells towards the bottom of the space. This occurs despite the use of hydrogel materials in 3D cell cultures, which would be expected to prevent this behavior. To better understand and explain these experimental observations, we conducted a multiscale experimental and mathematical examination of 3D cancer growth and sedimentation in triple negative breast cancer cells. The migration of cells towards the bottom was examined in the presence and absence of the migrastatic drug Paclitaxel, as well as in a low adhesion environment and the presence of fibroblasts. The observed behaviour was modeled mathematically by hypothesizing self-generated chemotactic gradients. Our results reveal that active migration mechanisms, specifically collective migration regulated by the MAPK and TGF-ß pathways, play an important role in sedimentation. The mathematical model was able to describe the experimental data in the absence and presence of Paclitaxel, suggesting the inhibition of random motion and advection mechanism in the latter case. Low adhesion environment and multiple cell type experiments resulted in an inhibition of sedimentation. Overall, our results suggest that cells, initially uniformly distributed in the 3D space, actively migrate towards the bottom due to the presence of signals produced by cells already attached to it, providing mechanistic insights into this unexpected behavior. Overall design: Comparative gene expression profiling analysis of RNA-seq data for Triple Negative Breast Cancer (TNBC) cells from the MDA-MB-231 cell line, non-treated and treated with Paclitaxel, grown in 3D Matrigel scaffold. The doses for the treated are: 0.5µ?, 0.05µ?, 0.005µM and 0.0005µ?. Samples were collected on days 2 and 4. Paclitaxel was administered on Day 2.