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Eg Phd, Mphil, Dclinpsychol This thesis has been submitted in fulfilment of the requirements for a postgraduate degree (e.g. PhD, MPhil, DClinPsychol) at the University of Edinburgh. Please note the following terms and conditions of use: This work is protected by copyright and other intellectual property rights, which are retained by the thesis author, unless otherwise stated. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author. The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author. When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Investigating miR‐214 as a pro‐fibrotic mediator in renal fibrosis and its potential as a therapeutic target via effective in vivo modelling of chronic kidney disease James O’Sullivan BSc. (Hons) Submitted in fulfilment of the requirements of the degree of Doctor of Philosophy in the College of Medicine and Veterinary Medicine, University of Edinburgh Centre for Cardiovascular Sciences, The Queen’s Medical Research Institute, College of Medicine and Veterinary Medicine, University of Edinburgh September 2019 Author’s Declaration I declare that this thesis was wrote entirely by myself and is composed of work carried out by myself, with the following exceptions. The work presented in this thesis has not been submitted for any other degree or professional qualification. For the purposes of my training, the majority of STNx surgeries for the chapter 4 study were carried out by Dr. Laura Denby. Sarah Finnie, Andrew Boyd, and Dr. Laura Denby assisted with the cull of animals in studies presented in chapters 3 and 4. Echocardiography imaging (chapter 4) was carried out by preclinical imaging technician Adrian Thompson (analysis of echocardiograph was carried out by myself). Biochemical analysis of serum and urine for albumin, creatinine, urea, and phosphate was carried out by Howie Forbes in the QMRI specialist biochemical analysis service. rUUO (chapter 5) surgeries were carried out by Gary Borthwick and Dr. Laura Denby, with Dr. Laura Denby carrying out sham and UUO group surgeries, while Gary Borthwick carried out the rUUO group surgeries. In the bulk rUUO RNA sequencing, RNA was extracted from whole kidney cortex, yield quantified via NanoDrop and quality assessed via Aglient Bioanalyser by Dr. Laura Denby and Carolynn Cairns. In relation to the RNA sequencing of FACS‐isolated renal cell populations (chapter 5), the protocol for preparing renal tissue for FACS, the use of the flow cytometer, RNA extraction, RNA quality and yield assessment via Aglient Bioanalyser, and amplified cDNA synthesis was carried out by Dr. Laura Denby and Carolynn Cairns. For RNA sequencing (chapter 5), library preparation, sequencing of libraries and quality control was carried out by Genewiz. IRI (chapter 5) and FACS process was carried out by Dr. Victoria Banwell, with RNA extraction carried out by myself and Dr. Victoria Banwell. James O’Sullivan September 2019 II Acknowledgements To my supervisor, Dr. Laura Denby, thank you for giving me the opportunity to learn and grow as a scientist over these four years. The advice and guidance you gave, as well as the space to explore my own ideas and interests, has allowed me to get to where I am today. Thank you to Prof. Andy Baker and Dr. Bryan Conway for the invaluable contributions and collaborations. For providing the funding that allowed me to do a PhD in the first place, I owe a debt of gratitude to Medical Research Scotland. I thank Regulus Therapeutics for generously co‐sponsoring my PhD and for inviting me to a three‐month placement in their lab, which was a great experience. Thank you to the other PhD students and staff who made the QMRI a bit more fun. Particularly to Rachel for the long coffee‐breaks, to Andrew for the random chats in the lab, and to Francesca for sharing my office‐related woes! Many members of my large family have, in some way, helped me get to the point where I’m finishing writing a PhD thesis, but a few in particular stand out. Thank you to my parents, who supported the earlier stages of this lengthy education of mine. During a recession was a pretty inconvenient time to go to college in Dublin, but we made it work. Thanks to Chloe and Conor, for always being there. Thank you to my Nanny O’Sullivan, for always, always, being there. To my Ada Wickham, thank you for telling me all the stories, teaching me so much about the world from a young age, and, of course, for bringing me to check the buoys. I owe a lot of the curiosity that drove me towards science to you. III Non scholæ, sed vitæ discimus. IV Table of Contents Author’s Declaration ............................................................................................. II Acknowledgements .............................................................................................. III Table of Contents .................................................................................................. V List of Figures ..................................................................................................... VIII List of Tables ......................................................................................................... XI Abstract ............................................................................................................... XII Lay Summary ....................................................................................................... XV List of Abbreviations ......................................................................................... XVIII Chapter One: General Introduction ..................................................................... 1‐1 1.1: Renal physiology ................................................................................................. 1‐2 1.2: Chronic kidney disease ........................................................................................ 1‐6 1.3: Markers of CKD ................................................................................................... 1‐7 1.3.1: Creatinine ........................................................................................................................ 1‐7 1.3.2: Cystatin C ......................................................................................................................... 1‐8 1.3.3: Albuminuria ..................................................................................................................... 1‐8 1.3.4: Serum phosphate .......................................................................................................... 1‐10 1.3.5: Serum urea .................................................................................................................... 1‐11 1.4: Cardiorenal syndrome ....................................................................................... 1‐12 1.5: Renal Fibrosis .................................................................................................... 1‐14 1.5.2: Cytokines and extracellular mediators in renal fibrosis ................................................ 1‐16 1.5.2.1: TGFβ ....................................................................................................................... 1‐16 1.5.2.2: Angiotensin II ......................................................................................................... 1‐17 1.5.2.3: TNFα ....................................................................................................................... 1‐18 1.5.3: Fibroblasts in renal fibrosis ............................................................................................ 1‐18 1.5.4: Macrophages in renal fibrosis ....................................................................................... 1‐22 1.5.5: Proximal tubular epithelial cells in renal fibrosis ........................................................... 1‐25 1.5.6: Endothelial cells in renal fibrosis ................................................................................... 1‐29 1.6: Animal models of renal injury ........................................................................... 1‐33 1.6.1: Unilateral ureteral obstruction (UUO) ........................................................................... 1‐33 1.6.2: Reversal of unilateral ureteral obstruction (rUUO) ....................................................... 1‐36 1.6.3: Subtotal nephrectomy ................................................................................................... 1‐38 1.6.4: Ischemia reperfusion injury (IRI) .................................................................................... 1‐41 1.7: microRNA ......................................................................................................... 1‐42 1.7.1: miRNA biogenesis and function ..................................................................................... 1‐42 1.7.2: miRNA in development .................................................................................................. 1‐46 1.7.3: miRNA in disease and as therapeutic targets ................................................................ 1‐47 1.8: miR‐214 in development, disease and homeostasis ........................................... 1‐49 1.8.1: miR‐214 in cardiac injury
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