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Genomic Characterization of Medulloblastoma Genomic Characterization of Medulloblastoma by Paul A. Northcott A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Laboratory Medicine & Pathobiology University of Toronto © Copyright by Paul A. Northcott 2010 Genomic Characterization of Medulloblastoma Paul A. Northcott Doctor of Philosophy Department of Laboratory Medicine & Pathobiology University of Toronto 2010 Abstract Medulloblastoma is the most common malignant pediatric brain tumour. Although survival rates have improved in recent years, long-term survivors exhibit a significantly diminished quality of life complicated by neurological, endocrine, intellectual, and social sequelae as a result of conventional therapies. In order to improve the current outlook for patients with medulloblastoma, rational, targeted therapies that are more efficient and less toxic are required. Despite insight gained from the study of hereditary tumour syndromes and candidate gene approaches, the molecular basis of medulloblastoma remains poorly defined, with more than half of all cases remaining unaccounted for at the genetic level. The intent of my PhD research program was to use high-resolution genomics in an attempt to gain an improved understanding of the medulloblastoma genome and potentially uncover novel genes and pathways driving its pathogenesis. By applying a combination of single nucleotide polymorphism (SNP) arrays, exon arrays, and microRNA arrays to a large cohort of primary medulloblastoma samples, we have identified novel oncogenes and tumour suppressors, implicated deregulation of the histone code as an important event in the pathogenesis of medulloblastoma, and refined the definition of medulloblastoma subgroups. This thesis demonstrates the extent of heterogeneity that exists in the medulloblastoma genome, showing that relatively few genomic aberrations are common when studying medulloblastoma as a single disease. In spite of this heterogeneity, we have identified novel candidate genes and processes that may serve as potential targets for future therapies. Importantly, we have established an improved method of classifying medulloblastomas into distinct molecular variants, showing that certain genomic changes are enriched and occasionally restricted to a ii specific subgroup. Finally, in addition to genomic differences, we have confirmed that medulloblastoma subgroups differ in their demographics and clinical behavior, and propose that medulloblastoma subgroup affiliation should become an integral component of patient stratification in the future. iii Acknowledgments First and foremost, I would like to thank my supervisor, Dr. Michael Taylor, for believing in me and giving me the opportunity to lead an outstanding PhD project in both a challenging and rewarding environment. I am also most grateful to have been co-supervised by Dr. Jim Rutka, who has provided me with important guidance and inspiration throughout the course of my thesis. I extend my gratitude to my additional supervisory committee members, Dr. Steve Scherer and Dr. Brent Derry, for their valuable insight and input towards my research. I am deeply indebted to all Taylor and Rutka Lab members, past and present, for their support, sharing of reagents and expertise, and willingness to contribute to my projects over the years. I would specifically like to acknowledge Paul Kongkham, Yukiko Nakahara, Xiaochong Wu, Stephen Mack, Adrian Dubuc, and John Peacock for their direct contributions to this thesis. I also thank Christian Smith for his invaluable “IT” support offered during the course of my PhD. From The Centre for Applied Genomics, I am grateful to Lars Feuk, Christian Marshall, John Wei, Chao Lu, Lan He, Kozue Otaka, and Xiaolin Wang for their amazing support with our genomics projects. From the Imaging Facility, I thank Paul Paroutis for assistance with microscopy and artwork. None of my PhD success would have been possible without strong collaborations with investigators and trainees from other institutions. I specifically thank Stefan Pfister, Hendrik Witt, Andrey Korshunov, Anna Kenney, Africa Fernandez, Charles Eberhart, Sidney Croul, and David Ellison for their collaboration. I would like to extend my gratitude to my family, including my mother Anne, and father Peter, for their endless support and encouragement to pursue success in life. Finally, I am most grateful to my wife Kara, and daughter Addison, for giving me daily inspiration and the motivation and strength to work hard and seek enjoyment in all aspects of life. iv Table of Contents !%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%" & %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%& &%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%& &%& %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% & &%' $ !# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%' .)/). ))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))0 .)/)/ )))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))3 .)/)0 ))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))4 .)/)1 + ))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))5 &%( $ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%+ .)0). )))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))6 .)0)/ ))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))6 .)0)0 )))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))).. .)0)1 )))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))./ .)0)2 '%'& ! )))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))).0 &%) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% &* .)1). !%%##"!%#% $"#)))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))).3 .)1)/ *!"$#"$"#(#!%#% '!!%* , -' "$# %! 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