134 Chapter 6 healing response, miscommunication between the epithelial and stromal cells, senescence of these cells as well as increased number of pro-fibrotic cells such as myofibroblasts or pro-fibrotic macrophages, are all thought to contribute to the perpetuation of the fibrotic response in the lung tissue [45, 46]. The changes in ECM in IPF and their associated influences on the cells are reviewed elsewhere [22, 23, 47-51]. Among these changes, greater deposition of collagens type I, III and VI are well documented in IPF patients compared to healthy controls [52]. Similarly, elastic fibers are more abundant in lung parenchyma of IPF patients compared to non-IPF controls [53, 54]. In addition to the increased deposition of ECM proteins, posttranslational modifications such as fiber crosslinking are more prominent in lung tissues of IPF patients compared to healthy controls [55, 56]. Lung biomechanical properties are altered as a result of changes in ECM structure: lung tissue of IPF patients are significantly stiffer compared to healthy tissue (16.52 ± 2.25 vs 1.96 ± 0.13 kPa), with an accompanying decrease in the viscoelastic relaxation properties (72.1 ± 13.1% vs 88.7 ± 10.4%)) [57, 58]. The instructiveness of ECM has been shown to provide a positive feedback loop between fibrotic ECM and fibroblasts [59-61]. Similar to other chronic lung diseases, secreted/released ECM fragments and growth factors deposited in ECM could also be playing crucial roles in the pathophysiology of IPF: increased TGF-β, latent TGF binding protein (LTBP) and several ECM protein degradation fragments have been found higher in IPF patients compared to healthy controls [62-64]. Likewise, IPF patients were found to have higher levels of fibulin-1 both in serum and lung tissue, compared to healthy controls [65]. In addition, the enzyme responsible for regulating crosslinking of collagen and elastin fibers, lysyl oxidases and transglutaminases are also recognized to be dysregulated in IPF [55, 60, 66]. In summary, the amounts and composition of ECM proteins present in the lung tissues are drastically altered in IPF, which also leads to biomechanical changes in the lung microenvironment. 2D VS 3D CELL CULTURE SYSTEMS 2D cell cultures have been used since the beginning of the 20th century. Basic 2D cell culture models include adherence of cells to petri dishes, tissue culture flasks or well plates made from glass or tissue-culture polystyrene. 2D culture systems described below do not consider suspension cell cultures. Classic 2D systems are simple to handle, easy to reproduce and facilitate the growth of large volumes of cells. Also, methods such as single-cell imaging and profiling of cells are easy to apply using such 2D-model culture systems. Moreover, 2D cell culture procedures are generally standardized and reproducible [67, 68] and these models are widely
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