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Elucidating the Genetic Basis of Canine Progressive Retinal Atrophies in Several Breeds of Dog

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Elucidating the Genetic Basis of Canine Progressive Retinal Atrophies in Several Breeds of Dog Rebekkah Jean Hitti-Malin Department of Veterinary Medicine Hughes Hall College University of Cambridge This thesis is submitted for the degree of Doctor of Philosophy May 2020 Declaration This thesis is the result of my own work and includes nothing which is the outcome of work done in collaboration except as declared in the Preface and specified in the text. It is not substantially the same as any that I have submitted, or, is being concurrently submitted for a degree or diploma or other qualification at the University of Cambridge or any other University or similar institution except as declared in the Preface and specified in the text. I further state that no substantial part of my thesis has already been submitted, or, is being concurrently submitted for any such degree, diploma or other qualification at the University of Cambridge or any other University or similar institution except as declared in the Preface and specified in the text. It does not exceed the prescribed word limit for the relevant Degree Committee. Signed: Date: 4th May 2020 Rebekkah Jean Hitti-Malin ii Elucidating the Genetic Basis of Canine Progressive Retinal Atrophies in Several Breeds of Dog Rebekkah Hitti-Malin Canine progressive retinal atrophies (PRA) are a group of hereditary diseases characterised by rod and cone photoreceptor cell death in the retina. This study sought to elucidate novel PRA- associated variants of distinct forms of PRA in three breeds of dog: the Lhasa Apso (LA), Giant Schnauzer (GS) and Shetland Sheepdog (SS). A genome-wide association study identified a 1.3 Mb disease-associated region on canine chromosome 33 in LA dogs. Whole genome sequencing (WGS) analysis of a PRA-affected LA revealed a long interspersed nuclear element-1 (LINE-1) insertion in the predicted promoter region of the retinal candidate gene, IMPG2. Validation of the LINE-1 insertion determined it segregated with disease and was likely to be private to LA dogs. Comprehensive WGS analyses alone were utilised to determine PRA-associated mutations in a family of GS dogs, and in a single SS. For the GS breed, WGS was performed on two affected siblings and both non-affected parents. Successive filtering, for autosomal recessive deleterious variants, against 568 canine genomes identified a single nucleotide variant (SNV) in the gene encoding NECAP endocytosis associated 1 (NECAP1): c.544G>A (p.G182R). Screening 5,130 canids revealed only the three PRA-affected GS were homozygous for the SNV, yet heterozygotes were identified in the GS breed and in other breeds of German ancestry. NECAP1 has not previously been associated with retinal degeneration; however, these findings, in parallel with known gene function, indicate NECAP1 should be considered as a strong candidate for retinal degeneration research in other species. Following WGS analysis of the single SS against 176 controls of other breeds, a c.1222G>C (p.A408P) SNV in the Bardet-Biedl syndrome 2 gene (BBS2) was identified. In addition to PRA, homozygotes exhibited features including an upturned nose, unusual coat and dental defects, proposing a novel syndromic form of canine PRA. This research has elucidated three novel PRA-associated mutations for which diagnostic DNA tests have been developed, offering breeders the opportunity to avoid producing PRA-affected dogs. Since PRA shares clinical features to human retinitis pigmentosa (RP) and other phenotypically similar retinal diseases, this study may offer novel insights for consideration in human as well as canine retinal degeneration research and gene therapies. iii Acknowledgements Firstly, my thanks go to my supervisors for making this thesis possible. Thank you to Dr Cathryn Mellersh for her outstanding support and guidance throughout my time at the Animal Health Trust. From the start of my career, she has been encouraging and patient in helping me achieve and progress, and has provided substantial advice and expertise. It has been a pleasure working with Cathryn, who has hugely impacted my scientific development and has made this PhD experience extremely rewarding and fulfilling. Thank you to Dr David Sargan, my supervisor at Cambridge, who has also provided immense support and advice throughout my PhD. David has provided me with a wealth of knowledge, and I am most grateful for his time he has dedicated to teaching and encouraging me to progress throughout this PhD. I would also like to thank my colleagues and friends in the Canine Genetics team at the Animal Health Trust, especially Dr Louise Burmeister and Dr Sally Ricketts for their kindness, advice and proofreading skills not only throughout this PhD, but in all aspects during my time at the Animal Health Trust. I am very grateful for their expertise and knowledge. Thanks also go to Dr Debbie Guest, my PhD mentor - our final year chats gave me confidence to explore new opportunities following my PhD studies. I am also hugely grateful to Debbie for her scientific expertise in cell techniques to help me tackle the luciferase assay experiments. Thank you to all the funders who supported this work financially, in particular the Animal Health Trust, the Kennel Club Charitable Trust and all dog owners, vets and breed clubs for their financial donations and submission of valuable research samples and phenotype information that enabled these studies to build a thesis. Last, but certainly not least, thank you to my incredible network of family and friends that have supported me throughout my PhD studies. To my Harley, my loving husband - you have always believed in me. Thank you for your encouragement and for keeping me grounded and sane throughout this PhD. To my parents, Nanny and sisters; thank you for your continuous love, help and support in whatever I pursue. iv Table of Contents Declaration ........................................................................................................................................................................... ii Abstract ................................................................................................................................................................................iii Acknowledgements .......................................................................................................................................................... iv Abbreviations ....................................................................................................................................................................xii List of Figures ................................................................................................................................................................. xvii List of Tables .....................................................................................................................................................................xix Chapter 1 Introduction ............................................................................................................................................ 1 1.1 The origin of domestic dog breeds .......................................................................................................... 1 1.2 The canine genome ........................................................................................................................................ 1 1.3 Genetic implications of intensive breeding ......................................................................................... 2 1.4 The canine eye ................................................................................................................................................. 3 1.5 The retina ........................................................................................................................................................... 4 Retinal pigment epithelium ................................................................................................................................. 5 Photoreceptors .......................................................................................................................................................... 6 The phototransduction cascade ......................................................................................................................... 8 The visual cycle ...................................................................................................................................................... 11 1.6 Pathways of photoreceptor degeneration......................................................................................... 12 Disruption of the photoreceptor outer segment ...................................................................................... 13 Metabolic overload ............................................................................................................................................... 13 Defects in the RPE ................................................................................................................................................. 14 Continuous activation of phototransduction ............................................................................................. 14 1.7 Human inherited retinal degenerations (IRDs) .............................................................................. 15 Retinitis pigmentosa (RP).................................................................................................................................
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