Gene expression profile of bioreactor-cultured cardiac cells: activation of morphogenetic pathways for tissue engineering

Cells grown in three-dimensional (3D) culture take on in vivo phenotypes and organize into tissue-like structures. Understanding the pathways and mechanisms contributing to this in vitro tissuegenesis is a critical goal of tissue engineering. To identify pathways relevant to cardiac tissue engineering, we compared mRNA expression profiles from bioreactor-cultured 3D aggregates of primary neonatal rat heart cells (NRHCs), which form layered structures similar to cardiac tissue, and standard plate-cultured NRHCs, which do not. In a series of two experiments, NRHCs were grown on solid microcarrier surfaces within clinostatically rotated polytetrafluoroethylene (PTFE) vessels and compared to parallel cultures grown on standard tissue culture plates without rotation. After 1, 4, and 6 days, gene expression profiles were analyzed using Affymetrix Rat Genome U34A (RG-U34A) arrays. The results were validated using real-time PCR, and the data set was filtered to generate a list of 93 probe sets that were substantially the same in replicate samples but substantially different between the bioreactor and plate groups. Cluster analysis indicated that the bioreactor and plate samples had similar expression patterns on day 1 but that these patterns diverged thereafter. Database for Annotation, Visualization, and Integrated Discovery (DAVID) analysis revealed a number of statistically significant gene groupings, including groups associated with muscle development and morphogenesis. Further analysis of the annotated gene list indicated that 13 of the 93 filtered genes were associated with endothelial cells, blood vessels, or angiogenesis. These results suggest that 3D aggregate culture of NRHCs in bioreactors is associated with the differential expression of morphogenic and angiogenic pathways similar to those seen during cardiac development.