Role of the co-transcriptional regulators Yap/Taz in the normal and fibrotic lung epithelia

Idiopathic pulmonary fibrosis (IPF) is a fatal disease that exhibits patterns of usual interstitial pneumonia with honeycombing. IPF is characterized by damaged distal lung epithelium with excessive tissue scarring and extracellular matrix remodeling. The etiology of IPF is unknown and current therapies cannot end or reverse disease progression. Aberrant reactivation of developmental pathways is evident in IPF. Among these developmental actors are the co-transcriptional regulators Yap and Taz (YT). YT modulate processes such as proliferation, differentiation, and organ size and are regulated by the Hippo pathway. YT do not have a DNA binding domain but act through interaction with other transcription factors (TFs). YT play a role in fibrotic fibroblasts, but their role is not yet known in the fibrotic lung epithelium. The aim of this thesis project is to develop the tools needed to explore the role of Hippo-YT in fibrotic lung epithelium and to identify the TFs that YT interact with to exert their various functions.We first developed a method to simultaneously isolate proximal and distal lung progenitor cells from an individual mouse with the aid of a 3D printed surgical guide and found that the precision of dissecting the lung lobes affects the purity of the isolated distal progenitors and how they behave in organoid assays. We further found the Hippo pathway to be dysregulated in the fibrotic lung epithelium which led to increases in nuclear YT as well as known downstream targets. Interestingly, we found epithelial YT signaling to be actively involved in extracellular matrix remodeling in the fibrotic lung epithelium through modulation of lysyl oxidase expression, a collagen crosslinking enzyme. Targeting YT in vivo using an FDA approved drug ameliorated the fibrotic phenotype, indicating that YT targeting may be an option to treat fibrosis. We further used cleavage under target and release using nuclease (CUT&RUN) to identify the exact motif sequences on the genome where complexes containing YT bind in the normal and fibrotic lung epithelial. We further identified putative TFs that are known to bind the motif sequences identified. We found that YT have different interaction partners in the proximal and distal lung epithelium and further identified specific YT interactions in the human fibrotic lung epithelium.This current research project sets the basis for the identification of exact targeting mechanisms for finding therapeutics for IPF. YT are known to be responsible for a wide range of biologic processes and targeting YT’s profibrotic activity and promoting their pro-regenerative activities may result in beneficial effects for IPF patients

Highlights of the ERS Lung Science Conference and Sleep and Breathing Conference 2021 and the new ECMC members

The Lung Science Conference (LSC) and the Sleep and Breathing Conference (SBC) are two conferences organised by the European Respiratory Society (ERS), the latter held in association with the European Sleep Research Society. This year, the LSC and SBC were both held in a virtual format with the participation of researchers and clinicians from around the world. The participation of Early Career Members (ECMs) was notable in both events: 216 of 363 (60%) delegates attending the LSC were under 40?years old, and 315 of 920 (34%) delegates were ?40?years of age at the SBC. Both conferences included outstanding talks on the most recent advances in respiratory medicine and science, oral/poster communication sessions on novel research, exciting opportunities to network with peers, and much more!This paper provides a brief overview of some of the most remarkable sessions of the LSC and SBC, written by ECMs attending the sessions.We also present the new members of the Early Career Member Committee (ECMC) of the ERS from Assemblies 1, 4, 10, 12 and 13, who were elected in the latest round of ERS elections. Welcome aboard

Generation of Human 3D Lung Tissue Cultures (3D-LTCs) for Disease Modeling

Translation of novel discoveries to human disease is limited by the availability of human tissue-based models of disease. Precision-cut lung slices (PCLS) used as 3D lung tissue cultures (3D-LTCs) represent an elegant and biologically highly relevant 3D cell culture model, which highly resemble in situ tissue due to their complexity, biomechanics and molecular composition. Tissue slicing is widely applied in various animal models. 3D-LTCs derived from human PCLS can be used to analyze responses to novel drugs, which might further help to better understand the mechanisms and functional effects of drugs in human tissue. The preparation of PCLS from surgically resected lung tissue samples of patients, who experienced lung lobectomy, increases the accessibility of diseased and peritumoral tissue. Here, we describe a detailed protocol for the generation of human PCLS from surgically resected soft-elastic patient lung tissue. Agarose was introduced into the bronchoalveolar space of the resectates, thus preserving lung structure and increasing the tissue's stiffness, which is crucial for subsequent slicing. 500 µm thick slices were prepared from the tissue block with a vibratome. Biopsy punches taken from PCLS ensure comparable tissue sample sizes and further increase the amount of tissue samples. The generated lung tissue cultures can be applied in a variety of studies in human lung biology, including the pathophysiology and mechanisms of different diseases, such as fibrotic processes at its best at (sub-)cellular levels. The highest benefit of the 3D-LTC ex vivo model is its close representation of the in situ human lung in respect of 3D tissue architecture, cell type diversity and lung anatomy as well as the potential for assessment of tissue from individual patients, which is relevant to further develop novel strategies for precision medicine

Simultaneous isolation of proximal and distal lung progenitor cells from individual mice using a 3D printed guide reduces proximal cell contamination of distal lung epithelial cell isolations

The respiratory epithelium consists of multiple, functionally distinct cell types and is maintained by regionally specific progenitor populations that repair the epithelium following injury. Several in vitro methods exist for studying lung epithelial repair using primary murine lung cells, but isolation methods are hampered by a lack of surface markers distinguishing epithelial progenitors along the respiratory epithelium. Here, we developed a 3D printed lobe divider (3DLD) to aid in simultaneous isolation of proximal versus distal lung epithelial progenitors from individual mice that give rise to differentiated epithelia in multiple in vitro assays. In contrast to 3DLD-isolated distal progenitor cells, commonly used manual tracheal ligation methods followed by lobe removal resulted in co-isolation of rare proximal cells with distal cells, which altered the transcriptional landscape and size distribution of distal organoids. The 3DLD aids in reproducible isolation of distal versus proximal progenitor populations and minimizes the potential for contaminating populations to confound in vitro assays

Isolation of high yield and quality RNA from human precision-cut lung slices for RNA-sequencing and computational integration with larger patient cohorts

Precision-cut lung slices (PCLS) have gained increasing interest as a model to study lung biology/disease and screening novel therapeutics. In particular, PCLS derived from human tissue can better recapitulate some aspects of lung biology/disease as compared to animal models. Several experimental readouts have been established for use with PCLS, but obtaining high yield and quality RNA for downstream analysis has remained challenging. This is particularly problematic for utilizing the power of next-generation sequencing techniques, such as RNA-sequencing (RNA-seq), for non-biased and high through-put analysis of PCLS human cohorts. In the current study, we present a novel approach for isolating high quality RNA from a small amount of tissue, including diseased human tissue, such as idiopathic pulmonary fibrosis (IPF). We show that the RNA isolated using this method has sufficient quality for RT-qPCR and RNA-seq analysis. Furthermore, the RNA-seq data from human PCLS could be used in several established computational pipelines, including deconvolution of bulk RNA-seq data using publicly available single-cell RNA-seq data. Deconvolution using Bisque revealed a diversity of cell populations in human PCLS, including several immune cell populations, which correlated with cell populations known to be present and aberrant in human disease

Applications and Approaches for Three-Dimensional Precision-Cut Lung Slices. Disease Modeling and Drug Discovery

Chronic lung diseases (CLDs), such as chronic obstructive pulmonary disease, interstitial lung disease, and lung cancer, are among the leading causes of morbidity globally and impose major health and financial burdens on patients and society. Effective treatments are scarce, and relevant human model systems to effectively study CLD pathomechanisms and thus discover and validate potential new targets and therapies are needed. Precision-cut lung slices (PCLS) from healthy and diseased human tissue represent one promising tool that can closely recapitulate the complexity of the lung's native environment, and recently, improved methodologies and accessibility to human tissue have led to an increased use of PCLS in CLD research. Here, we discuss approaches that use human PCLS to advance our understanding of CLD development, as well as drug discovery and validation for CLDs. PCLS enable investigators to study complex interactions among different cell types and the extracellular matrix in the native three-dimensional architecture of the lung. PCLS further allow for high-resolution (live) imaging of cellular functions in several dimensions. Importantly, PCLS can be derived from diseased lung tissue upon lung surgery or transplantation, thus allowing the study of CLDs in living human tissue. Moreover, CLDs can be modeled in PCLS derived from normal lung tissue to mimic the onset and progression of CLDs, complementing studies in end-stage diseased tissue. Altogether, PCLS are emerging as a remarkable tool to further bridge the gap between target identification and translation into clinical studies, and thus open novel avenues for future precision medicine approaches

Modeling fibrotic alveolar transitional cells with pluripotent stem cell-derived alveolar organoids

Repeated injury of the lung epithelium is proposed to be the main driver of idiopathic pulmonary fibrosis (IPF). However, available therapies do not specifically target the epithelium and human models of fibrotic epithelial damage with suitability for drug discovery are lacking. We developed a model of the aberrant epithelial reprogramming observed in IPF using alveolar organoids derived from human-induced pluripotent stem cells stimulated with a cocktail of pro-fibrotic and inflammatory cytokines. Deconvolution of RNA-seq data of alveolar organoids indicated that the fibrosis cocktail rapidly increased the proportion of transitional cell types including the KRT5-/KRT17+ aberrant basaloid phenotype recently identified in the lungs of IPF patients. We found that epithelial reprogramming and extracellular matrix (ECM) production persisted after removal of the fibrosis cocktail. We evaluated the effect of the two clinically approved compounds for IPF, nintedanib and pirfenidone, and found that they reduced the expression of ECM and pro-fibrotic mediators but did not completely reverse epithelial reprogramming. Thus, our system recapitulates key aspects of IPF and is a promising system for drug discovery