12 Chapter 1 AIM AND OUTLINE OF THIS THESIS The overarching aim of this thesis was to investigate and characterize the interactions between the fibrotic ECM and cells, to elucidate how these contribute to subsequent pro-fibrotic reactions. In Chapter 2, I outlined the changes in the composition, mechanics and organization of ECM during lung fibrosis and summarize the recent advances regarding how these changes might pave the way to a better understanding of fibrotic responses. In Chapter 3, I reported how collagen type XIV, an ECM protein, is involved in fibrotic lungs. While its role in the organization of fibrillar collagens was previously demonstrated, the status of collagen type XIV in IPF was not described prior. In this study, I investigated how the relative proportion of collagen type XIV protein is different in lungs of patients with IPF at the whole tissue level, as Ill as in specific tissue compartments. In Chapter 4, I critically summarized the cutting-edge technologies used to mimic lung microenvironments in three-dimensional (3D) in vitro conditions. After reviewing different in vitro tools, and their advantages and disadvantages, I discussed the challenges associated with such models. Moreover, I provided a detailed overview of the recent translational applications for each model and characterizations of such models. In Chapter 5, I investigated regenerative responses of cells isolated from the lungs of IPF patients and compared them to cells isolated from non-IPF lungs using an organoid model system. I hypothesized that supportive cells from the stromal niche/ microenvironment imprinted by a fibrotic ECM carry over their “lessons” and result in a dysregulated regenerative response of epithelial cells. I compared the number and size of organoids developed from unfractionated cells obtained from non-IPF lungs to IPF lungs. In addition, I isolated epithelial cells from these unfractionated cell populations to test their regenerative capacity without the influence of additional cells. In Chapter 6, I described the state-of-the-art status of 3D in vitro models used to mimic lung ECM. I explained the advantages of 3D over two-dimensional (2D) culture systems and exemplified the most commonly used materials to create a 3D in vitro lung microenvironment.
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