Abstract
Progressive fibrosing interstitial lung disease (PF-ILD) is characterized by irreversible scarring and inflammation of lung tissue, resulting in a gradual loss of pulmonary function and eventually respiratory failure. Despite therapeutic advances aimed at slowing disease progression and alleviation of symptoms, the absence of curative treatments, together with a lack of precision medicine tools for accurate treatment response monitoring, poses a significant challenge for patient management. Addressing these needs necessitates a comprehensive understanding of the cellular and molecular mechanisms underlying PF-ILD. This thesis utilized high-throughput omics techniques, including proteomics, single-cell transcriptomics, and radiomics, to a) develop a non-invasive approach for stratification of molecular response to antifibrotic treatment, and b) to characterize a revised in vivo model of chronic lung fibrosis aimed at recapitulating human disease hallmarks more accurately. Radiomics is a high-dimensional image analysis technique that provides quantitative insights into organ-scale pathophysiology based on the premise that the molecular landscape of tissues is reflected in medical imaging phenotypes. These links are described through radiomic features, which in sum generate digital disease fingerprints. By integrative analysis of computed tomography-derived radiomic features and tissue-derived proteome profiles (radioproteomics), this study demonstrated that radiomic signatures can stratify the degree of antifibrotic response to nintedanib in (experimental) fibrosing ILD. Importantly, the established radioproteomic signatures paralleled disease- and drug-specific biological pathway activity with high specificity, including extracellular matrix remodeling, cell cycle activity, wound healing, and metabolic activity. Evaluation of the preclinical molecular response-defining radiomic features in a cohort of nintedanib-treated PF-ILD patients accurately stratified patients based on their extent of lung function decline, thereby highlighting the translational potential for clinical application. In exploring a chronic lung fibrosis model, which simulates the recurrent cycles of injury and tissue repair of human disease through repetitive exposure to alveolar epithelial injuries, this study substantiated previous findings and revealed new insights into disease pathogenesis. The chronic model developed several disease hallmarks that are inadequately recapitulated in the established acute model, including the extent of alveolar remodeling, the presence of fibrotic honeycomb-like cysts lined with KRT5+ basal cells, and a heightened inflammatory background. Moreover, fibrotic regions exhibited elevated levels of KRT8+ differentiation intermediates, which are thought to adopt key roles in mediating fibrosis progression, as well as occurrence of CCSP+ club cell bronchiolization. These changes were accompanied by upregulation of pro-fibrotic, pro-inflammatory and apoptosis-related pathways. Importantly, the use of radioproteomic association modules further indicated differential regulation of wound healing, which could be independently verified on proteome level. Whereas long-term absence of recurrent injuries in the acute model resulted in transient fibrosis, the chronic model proved to be more resistant against spontaneous fibrosis resolution, exhibiting increased collagen deposition and better preservation of the disease typical changes on cellular level. Sustained upregulation of pro-fibrotic signatures, including fibroblast metaplasia, fatty acid metabolism, and epithelial-to-mesenchymal transition, further differentiated the chronic from the acute model. Collectively, this doctoral thesis advanced the understanding of PF-ILD pathogenesis and demonstrated the potential of radiomics as a surrogate for molecular response phenotypes. These findings hold promise for the development of novel therapeutic strategies and the refinement of experimental approaches for studying PF-ILD.
Lauer, David