Genomic and Morphological Changes of Neuroblastoma Cells in Response to Three-Dimensional Matrices

Advances in neural tissue engineering require a comprehensive understanding of neuronal growth in 3 dimensions. This study compared the gene expression of SH-SY5Y human neuroblastoma cells cultured in 3-dimensional (3D) with those cultured in 2-dimensional (2D) environments. Microarray analysis demonstrated that, in response to varying matrix geometry, SH-SY5Y cells exhibited differential expression of 1,766 genes in collagen I, including those relevant to cytoskeleton, extracellular matrix, and neurite outgrowth. Cells extended longer neurites in 3D collagen I cultures than in 2D. Real-time reverse transcriptase polymerase chain reaction experiments and morphological analysis comparing collagen I and Matrigel tested whether the differential growth and gene expression reflected influences of culture dimension or culture material. SH-SY5Y neuroblastoma cells responded to geometry by differentially regulating cell spreading and genes associated with actin in similar patterns for both materials; however, neurite outgrowth and the expression of the gene encoding for neurofilament varied with the type of material. Electron microscopy and mechanical analysis showed that collagen I was more fibrillar than Matrigel, with larger inter-fiber distance and higher stiffness. Taken together, these results suggest complex cell–material interactions, in which the dimension of the culture material influences gene expression and cell spreading and the structural and mechanical properties of the culture material influence gene expression and neurite outgrowth.