Rocker or Pump? Transcriptomic Response of Endothelial Cells Exposed to Peristaltic Pump-Based Unidirectional Flow vs. Rocker-Induced Bidirectional Flow

Rocking-platform perfusion systems rely on hydrostatic pressure differences to perfuse cells in organ-on-chip devices. These systems are popular due to their tubing-free design, which facilitates parallelization, an essential feature for drug discovery, precision medicine, and academic research. However, most of these systems generate bidirectional flow, which does not accurately replicate the physiological conditions experienced by endothelial cells (ECs) in the microvasculature. To address this limitation, pump-based systems are often employed to generate unidirectional flow, though they require external tubing, thereby limiting scalability compared to rocking platforms. In this study, we compared the transcriptomic responses of endothelial cells exposed to flow generated either by a rocking platform or a peristaltic pump, under matched average flow rates. Our results revealed distinct transcriptomic profiles induced by the two flow modalities, with hundreds of genes differentially expressed between the two conditions. After 4 hours of flow exposure, we observed an enrichment in signaling pathways including NF-κB, ERK, BMP and MAPK. Furthermore, after 24 hours of flow exposure, we identified significant changes in the genes involved in biological processes such as immune cell migration, angiogenesis and vascular and extracellular matrix remodeling, highlighting how different flow generated by pump or rokcer can shape endothelial cell behavior at the molecular level. Human umbilical vein endothelial cells between passage 4 and 6 were exposed to either pump-based unidirectional or rocker-induced bidirectional flow for 4h and 24h in three replicates. Bulk RNA-seq was performed to study the effect of flow type on the gene expression profile of the endothelial cells.