Modulated Gene Expression in 3D Cell Culture: Implications for Drug Discovery

In-vitro cell models are essential for validating the efficacy of drug candidates. However, large numbers of compounds are discontinued in subsequent phases of clinical studies. The reason for these failures is poor predictability of 2D cell cultures1, which could not mimic physiological conditions. Thus, it is important that the cell model used in testing drug candidates is physiologically relevant and closely mimics in-vivo conditions by expressing appropriate receptors, drug transporters and essential proteins for cell growth and survival.

Cells grown in 3D environment (3D scaffolds, 3D hydrogels, 3D multiwell plates and 3D bioreactors) influences the spatial organization of receptors and interactions with neighboring cells, thereby influencing the gene expression and cellular behavior2. A number of studies demonstrated that behaviors of cells in 3D cultures are similar to the in-vivo conditions; some of the genes and proteins which are modulated in 3D cultures  in comparison with 2D cultures across various cell lines are listed below.

Gene/Protein Name Primary cells/Cell Line Modulation in 3D culture References
Cell adhesion proteins C2C12, Skeletal myoblasts, Huh7, MCF-7 Increase 208367633 192159494 196043765 145329956
Metabolic & Cytoskeletal proteins HepG2, 3T3-L1 Increase 209250557, 158694248, 194027869
Antioxidant proteins MDCK Increase 2071800810
Cytoskeletal proteins Fibroblasts Increase 2080894011
Mesenchymal genes and Pro-metastatic genes 293T Increase 2061523812
Immune response and Apoptosis genes L1236 Increase 1791797213
Kinases MC3T3-E1 Increase 1797308314
Extracellular matrix and cell adhesion proteins Primary smooth muscle cells, Microvascular endothelial cells, Primary-Bronchi smooth muscle cells Increase 1885412215 168885916 1934643117
Osteogenesis proteins H1 (Human embryonic stem cells) Increase 1822455718
Iron Metabolism proteins, Mitochondrial proteins HepG2 Decrease 209250557
Kinases HT1080, MC3T3-E1 Decrease 1670757214 2050728419
Cytoskeletal proteins Smooth muscle cells and Fibroblasts, Primary human ovarian fibroblasts, Primary-Smooth muscle cell (arota) Decrease 2080894011 1844815620 1834236621
Cell division genes L1236 Decrease 1791797213
Extracellular matrix proteins Chondrocytes Decrease 2147950122




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