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Patient-derived tumor organoids have been established as promising tools for in vitro modelling of multiple tumors, including cholangiocarcinoma (CCA). However, organoids are commonly cultured in basement membrane extract (BME) which does not recapitulate the intricacies of the extracellular matrix (ECM). We combined CCA organoids (CCAOs) with native tumor and liver scaffolds, obtained by decellularization, to effectuate a model to study the interaction between epithelial tumor cells and their surrounding ECM. Decellularization resulted in removal of cells while preserving ECM structure and retaining important characteristics of the tissue origin, including stiffness and presence of desmoplasia. The transcriptome of CCAOs in a tumor scaffold much more resembled that of patient-paired CCA tissue in vivo compared to CCAOs cultured in BME or liver scaffolds. This was accompanied by an increase in chemoresistance to clinically-relevant chemotherapeutics. CCAOs in decellularized scaffolds revealed environment-dependent proliferation dynamics, driven by the occurrence of epithelial-mesenchymal transition. Furthermore, CCAOs initiated an environment-specific desmoplastic reaction by increasing production of multiple collagen types. In conclusion, convergence of organoid-based models with native ECM scaffolds will lead to better understanding of the in vivo tumor environment. STATEMENT OF SIGNIFICANCE: The extracellular matrix (ECM) influences various facets of tumor behavior. Understanding the exact role of the ECM in controlling tumor cell fate is pertinent to understand tumor progression and develop novel therapeutics. This is particularly the case for cholangiocarcinoma (CCA), whereby the ECM displays a distinct tumor environment, characterized by desmoplasia. However, current models to study the interaction between epithelial tumor cells and the environment are lacking. We have developed a fully patient-derived model encompassing CCA organoids (CCAOs) and human decellularized tumor and tumor-free liver ECM. The tumor ECM induced recapitulation of various aspects of CCA, including migration dynamics, transcriptome and proteome profiles, and chemoresistance. Lastly, we uncover that epithelial tumor cells contribute to matrix deposition, and that this phenomenon is dependent on the level of desmoplasia already present.

Human cholangiocyte organoids show great promise for regenerative therapies and in vitro modeling of bile duct development and diseases. However, the cystic organoids lack the branching morphology of intrahepatic bile ducts (IHBDs). Here, we report establishing human branching cholangiocyte organoid (BRCO) cultures. BRCOs self-organize into complex tubular structures resembling the IHBD architecture. Single-cell transcriptomics and functional analysis showed high similarity to primary cholangiocytes, and importantly, the branching growth mimics aspects of tubular development and is dependent on JAG1/NOTCH2 signaling. When applied to cholangiocarcinoma tumor organoids, the morphology changes to an in vitro morphology like primary tumors. Moreover, these branching cholangiocarcinoma organoids (BRCCAOs) better match the transcriptomic profile of primary tumors and showed increased chemoresistance to gemcitabine and cisplatin. In conclusion, BRCOs recapitulate a complex process of branching morphogenesis in vitro. This provides an improved model to study tubular formation, bile duct functionality, and associated biliary diseases.

Background A subset of individuals with allergic asthma develops a late phase response (LPR) to inhaled allergens, which is characterized by a prolonged airway obstruction, airway inflammation and airway hyperresponsiveness. The aim of this study was to identify changes in the plasma proteome and circulating hematopoietic progenitor cells associated with the LPR following inhaled allergen challenge. Methods Serial plasma samples from asthmatics undergoing inhaled allergen challenge were analyzed by mass spectrometry and immunosorbent assays. Peripheral blood mononuclear cells were analyzed by flow cytometry. Mass spectrometry data were analyzed using a linear regression to model the relationship between airway obstruction during the LPR and plasma proteome changes. Data from immunosorbent assays were analyzed using linear mixed models. Results Out of 396 proteins quantified in plasma, 150 showed a statistically significant change 23 h post allergen challenge. Among the most upregulated proteins were three protease inhibitors: alpha-1-antitrypsin, alpha-1-antichymotrypsin and plasma serine protease inhibitor. Altered levels of 13 proteins were associated with the LPR, including increased factor XIII A and decreased von Willebrand factor. No relationship was found between the LPR and changes in the proportions of classical, intermediate, and non-classical monocytes. Conclusions Allergic reactions to inhaled allergens in asthmatic subjects were associated with changes in a large proportion of the measured plasma proteome, whereof protease inhibitors showed the largest changes, likely to influence the inflammatory response. Many of the proteins altered in relation to the LPR are associated with coagulation, highlighting potential mechanistic targets for future treatments of type-2 asthma.

Vascular bio-scaffolds produced from decellularized tissue offer a promising material for treatment of several types of cardiovascular diseases. These materials have the potential to maintain the functional properties of the extracellular matrix (ECM), and allow for growth and remodeling in vivo. The most commonly used methods for decellularization are based on chemicals and enzymes combinations, which often damage the ECM and cause cytotoxic effects in vivo. Mild methods involving pressurized CO2-ethanol (EtOH)-based fluids, in a supercritical or near supercritical state, have been studied for decellularization of cardiovascular tissue, but results are controversial. Moreover, data are lacking on the amount and type of lipids remaining in the tissue. Here we show that pressurized CO2-EtOH-H2O fluids (average molar composition, ΧCO2 0.91) yielded close to complete removal of lipids from porcine pulmonary arteries, including a notably decrease of pro-inflammatory fatty acids. Pressurized CO2-limonene fluids (ΧCO2 0.88) and neat supercritical CO2 (scCO2) achieved the removal of 90% of triacylglycerides. Moreover, treatment of tissue with pressurized CO2-limonene followed by enzyme treatment, resulted in efficient DNA removal. The structure of elastic fibers was preserved after pressurized treatment, regardless solvent composition. In conclusion, pressurized CO2-ethanol fluids offer an efficient tool for delipidation in bio-scaffold production, while pressurized CO2-limonene fluids facilitate subsequent enzymatic removal of DNA.

Lung function is highly dependent on the structure of the lung parenchyma. Remodeling of the alveolar compartment is a central part of the pathology of chronic lung disease such as chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Pathological lung remodeling occurs as an interplay between cells and the extracellular matrix (ECM) which in addition to its structural role influence most aspects of cell behavior. This thesis aimed to improve on the available in vitro methods for studies of cell-ECM interaction in the alveolar compartment of the human lung. A technique to produce acellular lung slices for cell culture from clinical lung resection material with preservation of native 3-dimensional structure and ECM composition was established and evaluated. Protein turnover in cell cultures in decellularized lung slices (DLS) was analyzed by mass spectrometry implementing amino acids labeled with stable heavy isotopes to distinguish between cell and DLS derived ECM proteins. The work entailed study of ECM production of primary human lung fibroblasts and primary human alveolar epithelial type II cells (AECII) in DLS from derived from human lungs. In addition, a device for mechanical stretching of lungs slice cultures have been designed and evaluated. Fibroblasts and AECII cultured in DLS secreted ECM components that were incorporated in structure of the lung slices. Fibroblasts showed to be highly responsive to their extracellular milieu and when cultured in IPF derived ECM, they produced ECM recapitulating pathological alterations of the ECM scaffold. In a comparison with fibroblast culture on standard plastic tissue culture surfaces the deposition of ECM proteins was hampered compared DLS culture. DLS culture of AECII showed that these cells produced a wide array of ECM proteins including interstitial matrix components mostly associated with cells of mesenchymal origin. AECII from explanted healthy and end stage COPD lungs were almost indistinguishable in a proteomic evaluation and with limited transcriptomic differences. Healthy AECII did however display a significant plasticity in ECM production when stimulated with the profibrotic growth factor TGF-ß1, upregulating many markers of IPF remodeling. Finally, the novel stretch device proved to be compatible with lung slice culture and capable to induce a cellular stretch responses. This thesis provide insight into how lung ECM can dictate cellular function and presents new techniques for the study of interactions of cells and ECM lung parenchyma. The presented model systems have potential to improve on the in vivo relevance of preclinical experimental research by better representing normal and pathophysiological conditions. Finally, the description of a broad capacity for ECM production by alveolar epithelial cells raises interesting questions about their importance in alveolar ECM homeostasis pathological remodeling.

Bronchiolitis obliterans syndrome, a common form of chronic lung allograft dysfunction, is the major limitation to long-term survival after lung transplantation. The histologic correlate is progressive, fibrotic occlusion of small airways, obliterative bronchiolitis lesions, which ultimately lead to organ failure. The molecular composition of these lesions is unknown. In this sutdy, the protein composition of the lesions in explanted lungs from four end-stage bronchiolitis obliterans syndrome patients was analyzed using laser-capture microdissection and optimized sample preparation protocols for mass spectrometry. Immunohistochemistry and immunofluorescence were used to determine the spatial distribution of commonly identified proteins on the tissue level, and protein signatures for 14 obliterative bronchiolitis lesions were established. A set of 39 proteins, identified in >75% of lesions, included distinct structural proteins (collagen types IV and VI) and cellular components (actins, vimentin, and tryptase). Each respective lesion exhibited a unique composition of proteins (on average, n = 66 proteins), thereby mirroring the morphologic variation of the lesions. Antibody-based staining confirmed these mass spectrometry–based findings. The 14 analyzed obliterative bronchiolitis lesions showed variations in their protein content, but also common features. This study provides molecular and morphologic insights into the development of chronic rejection after lung transplantation. The protein patterns in the lesions were correlated to pathways of extracellular matrix organization, tissue development, and wound healing processes.

Background: Mast cells play an important role in asthma, however, the interactions between mast cells, fibroblasts and epithelial cells in idiopathic pulmonary fibrosis (IPF) are less known. The objectives were to investigate the effect of mast cells on fibroblast activity and migration of epithelial cells. Methods: Primary distally-derived lung fibroblasts obtained from IPF patients and healthy individuals were cultured with LAD2 mast cells or stimulated with the mast cell proteases tryptase and chymase for 72 hours. Human lung fibroblasts and mast cells were cultured on traditional cell culture plastics or decellularized human lung tissue slices (lung scaffolds) to create a more physiological milieu by providing an alveolar extracellular matrix. Released mediators were analyzed and further evaluated for effects on epithelial cell migration. Results: Tryptase increased IL-6, VEGF and HGF release whereas co-culture with mast cells increased IL-6 in healthy lung fibroblasts. VEGF-C release was significantly increased in IPF fibroblasts and further induced by mast cells compared to healthy fibroblasts. Tryptase induced fibroblast migration but mast cells did not promote a myofibroblast phenotype such as altered αSMA levels. Culture in lung scaffolds increased the release of HGF and VEGF compared to culture on plastic plates. Migration of A549 epithelial cells was significantly reduced by IL-6, while HGF and conditioned media from scaffold cultures with mast cells and fibroblasts promoted migration. Conclusions: Mast cells and tryptase increased fibroblast release of mediators that influenced epithelial migration. These data indicate a role of mast cells in the interplay between fibroblasts, epithelial cells and the alveolar extracellular matrix in the pathogenesis of lung diseases.

Decellularized tissues offer an excellent approach to study cell-ECM interaction in health and disease. We have used peripheral lung tissue from healthy individuals and idiopathic pulmonary fibrosis (IPF) patients. IPF is characterized by excessive matrix production and stiffening of the tissue. The aim was to examine temporal changes in the original ECM in healthy and IPF scaffolds and how these affect protein production of repopulating fibroblasts. Tissue slices (350µm) were decellularized using CHAPS to generate biological scaffolds, characterized by density, biomechanical properties, histology, and mass spectrometry (MS). Scaffolds were mounted on custom-made holders, to mimic the native setting, seeded with human primary fibroblasts derived from a healthy donor, and cultured using medium supplemented with isotope-labeled Arg and Lys. Repopulated scaffolds were examined as described above to study differences in ECM. Heavy isotope labelling of cultured cells allowed us to follow up- and downregulation of newly synthesized proteins compared to original scaffold due to a mass shift detectable in MS. Interestingly, fibroblasts cultured on IPF scaffolds had a protein production profile overlapping with the profile of the original scaffold. Our biological system allowed us to study temporal differences in protein production in healthy and diseased scaffolds. By culturing under static stretch we created a 3D environment similar to the native situation, strongly influencing the cellular response. This opens up for in depth identification of proteins involved in lung disease and tissue regeneration. Our goal is to identify a combination of factors that can locally trigger a healthy lung regeneration.

In idiopathic pulmonary fibrosis (IPF) structural properties of the extracellular matrix (ECM) are altered and influence cellular responses through cell-matrix interactions. Scaffolds (decellularized tissue) derived from subpleural healthy and IPF lungs were examined regarding biomechanical properties and ECM composition of proteins (the matrisome). Scaffolds were repopulated with healthy fibroblasts cultured under static stretch with heavy isotope amino acids (SILAC), to examine newly synthesized proteins over time. IPF scaffolds were characterized by increased tissue density, stiffness, ultimate force, and differential expressions of matrisome proteins compared to healthy scaffolds. Collagens, proteoglycans, and ECM glycoproteins were increased in IPF scaffolds, however while specific basement membrane (BM) proteins such as laminins and collagen IV were decreased, nidogen-2 was also increased. Findings were confirmed with histology, clearly showing a disorganized BM. Fibroblasts produced scaffold-specific proteins mimicking preexisting scaffold composition, where 11 out of 20 BM proteins were differentially expressed, along with increased periostin and proteoglycans production. We demonstrate how matrisome changes affect fibroblast activity using novel approaches to study temporal differences, where IPF scaffolds support a disorganized BM and upregulation of disease-associated proteins. These matrix-directed cellular responses emphasize the IPF matrisome and specifically the BM components as important factors for disease progression.

Pulmonary artery grafts are needed as cardiovascular bioprosthetics. For successful tissue recellularization after transplantation, lipids have to be removed from the donor artery. Developing a selective process to remove lipids without damaging the extracellular matrix greatly depends on knowing the amount and type of lipid compounds in the specific tissue. Here we present an efficient methodology for the study of lipids present in porcine pulmonary arteries. The performance of six extraction methods to recover lipids from artery was evaluated. For this purpose, a supercritical fluid chromatography method coupled to quadrupole time-of-flight mass spectrometry detection (UHPSFC/QTOF-MS) was adapted. The method enabled separation of lipids of a wide range of polarity according to lipid class in less than 7 min. One dichloromethane-based extraction method was shown to be the most efficient one for the recovery of lipids from pulmonary artery. However, one MTBE-based extraction method was able to show the highest fatty acid extraction yields (to the expense of longer extraction times). Lipids were relative quantified according to class, and the major species within each class were identified. Triacylglycerols and glycerophospholipids were the most abundant classes, followed by sphingomyelins, monoacylglycerols and fatty acyls. The matrix effect exerted no interference on the analytical method, except for some few combinations of extraction method and lipid class. These results are of relevance for lipidomic studies from solid tissue, in particular for studies on pulmonary and cardiovascular diseases. Finally, our work sets the basis for the further development of a selective processes to remove lipids from pulmonary artery without damaging the tissue prior to transplantation.

Idiopathic pulmonary fibrosis (IPF) is a devastating lung disease associated with heterogeneous and abnormal build-up of extracellular matrix (ECM) proteins and increased fibroblast activity. We hypothesize that the alteration in material properties of lung tissue is one of the driving forces in the disease, where ECM stiffening has a fundamental impact on cellular responses. Our aim is to find a correlation between structural alterations of the ECM and cellular mechanisms associated with disease pathology such as increased proliferation, ECM synthesis and mechanotransduction. Thinly sliced distal tissue (350µm x 1cm2) from healthy (n=4) respective IPF (n=4) subjects was decellularized using a detergent-based protocol to produce acellular scaffolds. The scaffolds were characterized with histology, SEM, mass spectrometry, measurements of DNA content, tissue density and tensile strength. Next, the scaffolds were mounted in a holder, seeded with primary human fibroblasts from healthy donors and cultured for 9 days. Metabolic activity was measured after 1, 3, 6, and 9 days, with collection of histology samples at day 1 and 9. DNA content and tensile strength were measured after 9 days. The IPF-derived scaffolds displayed denser morphology with higher matrix stiffness in comparison to healthy tissue scaffolds. Mass spectrometric characterization of scaffolds separated IPF and healthy scaffolds into two cluster groups. Repopulated scaffolds displayed increased fibroblast proliferation and tissue stiffness over time. Further evaluations are performed to clarify the regulation of mechanotransduction and its association to pathological characteristics of the IPF matrisome.

Background Mast cells may activate fibroblasts and contribute to remodeling processes in the lung. However, the mechanism behind these actions needs to be further investigated. Fibroblasts are major regulators of on-going remodeling processes. Protease activated receptor 2 (PAR2) expressed by fibroblasts may be activated by serine proteases, such as the mast cell mediator tryptase. The objective in this study was to investigate the effects of mast cells and specifically mast cell tryptase on fibroblast migration and the role of PAR2 activation. Methods Human lung fibroblasts (HFL-1) were cultured together with human peripheral blood-derived mast cells or LAD2 mast cells and stimulated with either conditioned medium from LAD2 cells or tryptase. Analyses of immunological stimulation of mast cells by IgE/anti IgE in the co-culture system were also performed. The importance of PAR2 activation by mast cells and mast cell tryptase for the migratory effects of fibroblasts was investigated by pre-treatment with the PAR2 antagonist P2pal-18S. The expression of PAR2 was analyzed on fibroblasts and mast cells. Results The migratory capacity of HFL-1 cells was enhanced by blood-derived mast cells (p

Remodelling of the extracellular matrix is accomplished by altering the balance between matrix macromolecule production and degradation. However, it is not well understood how cells balance production of new matrix molecules and degradation of existing ones during tissue remodelling and regeneration. In this study, we used decellularized lung scaffolds repopulated with allogenic lung fibroblasts cultured with stable isotope labelled amino acids to quantify the balance between matrix production and degradation at a proteome-wide scale. Specific temporal dynamics of different matrisome proteins were found to correspond to the proliferative activity of the repopulating cells and the degree of extracellular deposition. The remodeling of the scaffold was characterized by an initial phase with cell proliferation and high production of cell adhesion proteins such as emilin-1 and fibronectin. Extended culture time resulted in increased levels of core matrisome proteins. In a comparison with monolayer cultures on plastic, culture in lung scaffolds lead to a pronounced accumulation of proteoglycans, such as versican and decorin, resulting in regeneration of an extracellular matrix with greater resemblance to native lung tissue compared to standard monolayer cultures. Collectively, the study presents a promising technique for increasing the understanding of cell- extracellular matrix interactions under healthy and diseased conditions.