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Choroid Plexus Tumours: Elucidating the Genomic Complexity of Rare Paediatric Brain Tumours

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Choroid Plexus Tumours: Elucidating the Genomic Complexity of Rare Paediatric Brain Tumours Choroid Plexus Tumours: Elucidating the Genomic Complexity of Rare Paediatric Brain Tumours by Diana Margarita Merino A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Medical Biophysics University of Toronto © Copyright by Diana M. Merino 2015 Choroid Plexus Tumours: Elucidating the Genomic Complexity of Rare Paediatric Brain Tumours Diana M. Merino Doctor of Philosophy Department of Medical Biophysics University of Toronto 2015 Abstract Choroid plexus tumours (CPTs) are rare intraventricular neoplasms, most commonly found in children, with variable clinical presentation and patient outcome. CPT biology is poorly understood largely due to limited tumour availability and the lack of accurate in-vitro and in-vivo models of disease. My thesis work focused on elucidating the molecular alterations of these rare tumours using high-throughput approaches that enabled the identification of recurrent alterations affecting CPTs and facilitated the classification of clinically and molecularly distinct CPT subgroups. Chapter 1 describes the current clinical and biological understanding of CPTs, providing a background on what’s currently known and identifying research gaps addressed in future chapters. Chapter 2 describes the molecular landscape of CPTs, achieved by defining patterns in copy number, gene expression and DNA methylation, as well as telomere lengthening mechanisms observed in these tumours. Chapter 3 describes the creation of a novel mouse model of CPC and the identification of novel oncogenes involved in CPC development using a cross- species genomics approach. Chapter 4 examines future directions in choroid plexus research and suggests novel avenues to pursue in order to improve our collective understanding on the ii mechanisms driving CPC development and how to best approach the clinical management of patients with CPC. The aim of this thesis is to highlight recent advances in CPT biology and to provide the molecular framework on which to build an evidence-based treatment strategy to effectively diagnose and treat patients affected by the disease. iii Acknowledgments None of this work would have been possible without the support and commitment of extraordinary people who played a key role in the completion of my degree. Thank you to my supervisor, Dr. David Malkin, for believing in me, for supporting me, providing me with personal and professional development opportunities, and for exemplifying how one can transform and make a difference in childhood cancer care. Your commitment to helping others is inspiring. I have learnt extensively from you and the dedication and integrity you demonstrate in everything you do. Thank you to the members of my supervisory committee Drs. Thomas Kislinger, Stephen Meyn, and Michael Taylor, for their expertise, guidance and sincere advice. I have had the blessing to meet extraordinary collaborators and work alongside them during my thesis project. Thank you to Dr. Richard Gilbertson for his guidance and support, and for mentoring me and opening the doors of his laboratory during my research exchange at St. Jude Children’s Research Hospital. Thank you to the Gilbertson laboratory for their patience and guidance during my time training there. Thank you to Dr. Uri Tabori, for his sincere and accurate feedback and for his expert advice. Thank you to Dr. Jan Korbel for opening the doors of his laboratory at the European Molecular Biology Laboratories (EMBL) so that I can learn analytical techniques, and thank you to the Korbel laboratory for their guidance and support. Thank you to my research mentors, Drs. Stephen Mack, Marc Remke, Vijay Ramaswamy, and Adam Shlien, for their guidance, support and intellectual discussions over coffee. Thank you to my Malkin lab family, past and present, for your amazing support. You have helped me keep my calm through it all. I will never forget our time together, especially the iv legendary Christmas gift presentations, birthday celebrations and GGB picnics. Thank you to the BTRC, for making me feel like one of your own and helping me with research ideas, advice and distractions. This thesis is dedicated to my Lord and Saviour Jesus Christ, to whom I owe the gift of life, grace and hope, and for giving me the ability to work on something I enjoy so much; and to my family, who has supported, encouraged, and kept me grounded during this PhD journey. Mom and Dad, you have shown me what true wisdom is all about, you have encouraged me to follow my dreams, no matter how big they may be, and to fight for those dreams with determination while keeping my eyes fixed on things of above. Diego, Rachel and Daniel, thank you for always being there for me, for listening to my science and providing a much needed and refreshing point of view. You have influenced my life in more ways than you realize. Leora Valentina, thank you for filling this last year with your giggles and for reminding me about the miracle of life. To my friends, for helping me find joy in the small things, for your listening ears and for all the memories we have created and now share. Thank you for reminding me that life is not a sprint, but a marathon. Lastly, I would like to dedicate this work to cancer patients and survivors whose generosity and cooperation allows us to investigate this disease more profoundly, and whose determination in fighting this disease inspire and motivate me to make a difference in this field. Thank you. v Table of Contents Abstract .......................................................................................................................................... ii Acknowledgments ........................................................................................................................ iv Table of Contents ......................................................................................................................... vi List of Tables ............................................................................................................................... xii List of Figures ............................................................................................................................. xiii Chapter 1: Introduction ............................................................................................................... 1 1. Acknowledgements ................................................................................................................ 1 2. The choroid plexus ................................................................................................................. 1 2.1. Function ................................................................................................................................................. 2 2.2. Development ........................................................................................................................................ 3 2.3. Disease .................................................................................................................................................... 3 3. Tumours of the choroid plexus ............................................................................................. 3 3.1. Demographic characteristics of CPT patients ........................................................................... 4 3.2. Classification of CPTs ......................................................................................................................... 6 3.2.1. Pathology ............................................................................................................................................................ 6 3.2.2. Immunohistochemistry ................................................................................................................................ 7 3.3. Clinical presentation ......................................................................................................................... 7 3.4. Clinical outcomes of CPT patients ................................................................................................. 8 4. TP53-more than just a tumour suppressor gene ................................................................. 9 4.1. TP53: The guardian of the genome ............................................................................................... 9 4.2. TP53 and tumourigenesis ................................................................................................................ 9 4.3. Mutant TP53 and its oncogenic role ........................................................................................... 11 5. Choroid plexus tumours and familial cancer syndromes ................................................. 12 5.1. CPC and the Li-Fraumeni syndrome ........................................................................................... 12 5.2. CPTs and genetic disease ............................................................................................................... 13 6. Genomic instability in cancer: aneuploidy and chromothripsis ...................................... 14 vi 6.1. Aneuploidy: causes and consequences ...................................................................................... 14 6.1.1. Causes of aneuploidy .................................................................................................................................. 15 6.1.2. Consequences of aneuploidy .................................................................................................................
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