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Developing a 3D Model of the Airways

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Developing a 3D Model of the Airways Developing a 3D Model of the Airways A thesis submitted for the degree of Doctor of Philosophy (PhD) Tankut G. Güney Airway Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW3 6LY 1 Abstract Chronic cigarette smoke exposure leads to chronic obstructive pulmonary disease (COPD) in susceptible individuals where goblet cell metaplasia, ciliated cell hypoplasia and extra cellular matrix (ECM) thickening are observed. Current in vitro COPD models such as air-liquid interface (ALI) cultures, cannot model the complex morphology and the cell-ECM interaction seen in vivo. No organoid models of COPD currently exist and, therefore, a lung organoid model termed bronchosphere of COPD was generated. Basal epithelial cells from normal healthy and COPD donors were cultured into bronchospheres over 20 days in 25% Matrigel. Bronchospheres were characterised using quantitative PCR, immunofluorescence and RNA sequencing. The effect of stromal cells on basal epithelial cell-derived bronchosphere structure and function were investigated through a triple culture of bronchial epithelial, lung fibroblast and airway smooth muscle cells. COPD bronchospheres developed more slowly displaying goblet cell hyperplasia and ciliated cell hypoplasia with reduced cilial beat frequencies compared to normal healthy controls. Normal healthy basal cells chronically treated with cigarette smoke condensate formed bronchospheres with lumens lacking a differentiated epithelium. RNA-seq analysis of bronchospheres showed up-regulation of the club cell markers mucin 5B (muc5b) and secretoglobin family 3A member 1 (scgb3a1) in healthy vs COPD bronchospheres. Pathway analysis revealed increased extracellular matrix function and decreased fibroblast growth factor signalling in COPD and cigarette smoke-treated healthy bronchospheres, which may be a possible driver of disease phenotype. Epithelial-stromal cross talk enabled formation of epithelial cell-driven branching tubules consisting of luminal epithelial cells surrounded by stromal cells. Addition of agarose to the Matrigel scaffold (Agrigel) altered the matrix viscoelasticity and stiffness and prevented tubule collapse. This thesis described the development of a novel bronchosphere model of COPD derived from primary human airway cells that recapitulates many functions of human COPD. Generating large numbers of these bronchospheres provides opportunities for future personalised drug testing. 2 Declaration of originality I, Tankut G. Güney declare that I wrote this thesis and the experiments and work described herein, except where appropriately referenced, was performed by myself. Information derived from the published and unpublished work of others has been acknowledged in the text and full references are given. Copyright declaration ‘The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Derivatives licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or redistribution, researchers must make clear to others the licence terms of this work’. 3 Acknowledgements I would like to give my sincerest heartfelt thank you to my supervisors Professor Ian Adcock and Dr Sharon Mumby for their tremendous support over the past 4 years. Thank you for sharing your knowledge and giving me the space to drive this project forward. I would like to thank my secondary supervisor Dr Mark Dowling and the NIBR team Dr Kevin White and Kaushik Subramanian for helping me formulate a project and making the best of my time in Boston - I had a blast! I would also like to thank Dr Vera Ruda for running the RNA-seq. I would like to extend my gratitude to Dr Iain Dunlop and Alfonso Herranz for helping me formulate a new scaffold and letting me use their facilities. My thanks also go to Vahid Elyasigomari for showing me how to do RNA-seq analysis. I would also like to thank Dr Rebecca Holloway for allowing me to teach the knowledge I gained in lab at Outreach. You really allowed me to develop a passion for teaching. Furthermore, I would like to thank my friends Dr Sarah Christen, Dr Elaina Maginn, Dr Abel Tesfai, Nicholas Wood and Dr Elisa Zanini for pulling me out of lab and showing me a world beyond my work. Thank you to Daniel Browne and Miranda Debenham for their enthusiasm in listening to updates on my project at our weekly ‘Lung News’ segment during our D&D games. Also, to Dr Nathalie Schmidt for her insight during our coffee meetings. Thank you to Christian and Dr Andrea Dungl for their support during my 4 years. Finally, words cannot express how immensely grateful I am to my fiancée Daniela Dungl and to my mother Betigül Güney who have shown love, patience, kindness and understanding during my PhD. A special thank you to my mother who has always championed me and pushed me to achieve my best. I dedicate this thesis to you both. 4 Table of Contents Abbreviations ................................................................................................... 15 Chapter 1 Introduction .................................................................................... 26 1.1 Chronic obstructive pulmonary disease (COPD) .................................. 27 1.1.1 Definition, Risk factors and prevalence .......................................... 27 1.1.2 COPD Pathophysiology ................................................................. 29 1.2 Lung Morphology and Development ..................................................... 31 1.2.1 Overview of Lung Development ..................................................... 31 1.2.2 Branching Morphogenesis ............................................................. 32 1.2.3 The Extracellular Matrix (ECM) ...................................................... 37 1.2.4 Luminogenesis ............................................................................... 45 1.3 Lung Epithelial Cell Populations ........................................................... 50 1.3.1 Airway Smooth Muscle (ASM) Development ................................. 53 1.4 Airway Regeneration, Repair and COPD.............................................. 54 1.5 Current Models of the Airway ............................................................... 58 1.5.1 Murine Models ............................................................................... 59 1.5.2 2D Models of Lung Disease ........................................................... 59 1.5.3 Organoid Models ............................................................................ 61 1.5.4 Future Directions ............................................................................ 64 1.6 Hypothesis ............................................................................................ 66 1.6.1 Aims ............................................................................................... 67 2 Chapter 2 Methodology ........................................................................... 68 2.1 Monolayer Cell Culture ......................................................................... 69 2.1.1 HBE cell culture.............................................................................. 69 2.1.2 Stromal cell culture ......................................................................... 70 5 2.1.3 Feeder Layer Culture ..................................................................... 71 2.1.4 HBE-3T3 cell co-culture ................................................................. 71 2.2 Bronchosphere Culture ......................................................................... 73 2.3 Bronchotubule Culture .......................................................................... 74 2.3.1 Matrigel Overlay Culture ................................................................ 74 2.3.2 Matrigel Triple Culture .................................................................... 75 2.3.3 Agrigel* (agarose-matrigel mix) Culture ......................................... 76 2.4 Generation of Cigarette Smoke Condensate (CSC) ............................. 78 2.5 Cell Viability Assay ............................................................................... 79 2.6 Cilia Beat Frequency (CBF) .................................................................. 79 2.7 Bronchosphere RNA Extraction ............................................................ 80 2.7.1 Bronchosphere Isolation, lysis and homogenisation ...................... 80 2.7.2 RNA Extraction .............................................................................. 81 2.7.3 Reverse transcription ..................................................................... 82 2.8 Immunofluorescence (IF) Staining ........................................................ 83 2.9 Maxiprep Plasmid Purification and Plasmid Generation ....................... 84 2.9.1 Lentiviral Generation ...................................................................... 86 2.10Rheometry of Agarose, Matrigel and Agrigel ........................................ 88 2.11RNA-Seq Bioinformatics ....................................................................... 89 2.12Statistical Analysis ................................................................................ 89 3 Chapter 3 Bronchosphere Model Development and Characterisation ..... 90 3.0 Introduction ..........................................................................................
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