Alginate hydrogels have been used as a
biomaterial for 3D culturing for several years. Here, gene expression patterns in
melanoma cells cultivated in 3D
alginate are compared to 2D cultures. It is well-known that 2D cell culture is not resembling the complex in vivo situation well. However, the use of very intricate 3D models does not allow performing high-throughput screening and analysis is highly complex. 3D cell culture strategies in
hydrogels will better mimic the in vivo situation while they maintain feasibility for large-scale analysis. As
alginate is an easy-to-use material and due to its favorable properties, it is commonly applied as a bioink component in the growing field of cell encapsulation and biofabrication. Yet, only a little information about the transcriptome in 3D cultures in
hydrogels like
alginate is available. In this study, changes in the transcriptome based on
RNA-Seq data by cultivating
melanoma cells in 3D
alginate are analyzed and reveal marked changes compared to cells cultured on usual 2D tissue culture
plastic. Deregulated genes represent valuable cues to signaling pathways and molecules affected by the culture method. Using this as a model system for
tumor cell plasticity and heterogeneity, EGR1 is determined to play an important role in
melanoma progression.