Alteration in gene expression patterns and increased drug resistance in MCF7 breast cancer cells cultured on 3D collagen-based scaffolds.

2D models have been instrumental in breast cancer research and advancing our knowledge of the disease, both in terms of progression and treatment. However, they fail to replicate the three-dimensional (3D) architectural and microenvironmental properties that influence tumour behaviour in vivo and response to therapy. To overcome these limitations, 3D culture models have emerged as valuable tools in cancer research. These 3D models provide a more physiologically relevant environment by allowing cells to grow in a three-dimensional structure that better replicates the tumour microenvironment. Here we demonstrated significant alterations in gene expressions in breast cancer cells cultured in a 3D collagen-gelatin scaffold compared to 2D cultured cells. In addition, we successfully applied the scaffolds as a test bed for therapeutic agents, demonstrating a significant increase in chemoresistance upon culture in the collagen-gelatin scaffolds (2D relative IC50 of 0.00028 μM vs. 3D scaffold IC50 of 0.00045 μM, 60.7 % increase). Genes associated with extracellular matrix (ECM) modification and synthesis, glycolysis, hypoxia and tumour survival had elevated expression levels in the 3D culture of MCF7 cells, indicating a switch to a more aggressive phenotype. Furthermore, we demonstrated for the first time the importance of the adaption period to the 3D environment, with resistance to docetaxel acquired as a function of cell pre-culture time within the scaffold. Overall, the findings herein demonstrate how 3D collagen scaffolds can potentially bridge the gap between 2D culture and animal models, through more accurately modelling the gene expression profiles of cancer cells and their response to therapeutic agents.