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Molecular Genetic Characterization of Ovarian Tumors

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Molecular genetic characterization of ovarian tumors Thesis for the degree of Philosophiae Doctor (PhD) University of Oslo, 2018 Antonio Agostini Section for Cancer Cytogenetics Institute for Cancer Genetics and Informatics The Norwegian Radium Hospital Oslo University Hospital Department of Biosciences Faculty of Mathematics and Natural Sciences University of Oslo The Norwegian Cancer Society Radium Hospital Foundation © Antonio Agostini, 2018 Series of dissertations submitted to the Faculty of Mathematics and Natural Sciences, University of Oslo No. 1992 ISSN 1501-7710 All rights reserved. No part of this publication may be reproduced or transmitted, in any form or by any means, without permission. Cover: Hanne Baadsgaard Utigard. Print production: Reprosentralen, University of Oslo. Molecular genetic characterization of ovarian tumors Antonio Agostini University of Oslo 2018 1 Cover Illustration Bellerophon fighting the Chimera, Roman mosaic, 1st century A.D. (Image from Wikimedia commons) Bellerophon was one of the most ancient heroes of Greek mythology and a monster hunter. One day King Iobates gave Bellerophon an impossible quest: to hunt the Chimera, a fire- breathing monster. The Chimera was truly ferocious, and Bellerophon could not harm the monster even if he was riding Pegasus, the winged horse. Feeling the heat of the breath of the Chimera, an idea struck him: He got a large block of lead that he mounted on his spear. Then he flew head-on towards the Chimera and managed to lodge the block of lead inside the monster's jaws. The lead melted in the monster’s throat and killed the Chimera. Finally Bellerophon returned victorious to King Iobates. Nora Heisterkamp and colleagues in 1983 described the first chimeric, cancer-specific gene, BCR-ABL1, originating from the translocation t(9;22)(q34;11) in chronic myeloid leukemia. Since then many other fusion genes were discovered and found to be primary events in the pathogenesis of different types of cancer. Nowadays the hunt for these chimeras goes on with the help of ever more advanced technologies. 3 Acknowledgements The work described in this thesis was performed at the Section of Cancer Genetics, Institute of Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo. The studies were funded by grants from the Norwegian Radium Hospital Foundation, the Norwegian Cancer Society, the Center for Cancer Biomedicine, the John and Inger Fredriksen Foundation, and the Anders Jahre’s foundation through UNIFOR (University of Oslo). I would first like to thank my main supervisor, Francesca Micci, for giving me the opportunity of working in one of the best cytogenetic group in the world. You are a great leader, mentor, and friend. I also want to thank you for your continuous support and guidance; and for having entrusted me such interesting, complicated but fun, studies. The second person that I want to thank is Ioannis Panagopoulos. I want to thank you for everything you taught me about fusion genes, for always encouraging me; and for all the fun times we had. Anyway, you will never convince me that Greeks were better than Romans. Marta Brunetti deserves special thanks for having helped me with the research projects presented here. I want to thank you for your collaboration and friendship. I want to thank Sverre Heim for having shown me the beauty of chromosomes, and for all the funny and interesting history lessons. But most of all I want to thank you for your contribution in the writing process of articles and thesis. I would like to thanks all the co-authors of the papers presented in this thesis. In particular I want to thank Ben Davidson for providing the patients’ material and his contributions in my research projects. I want to thank all my colleagues at the Section for Cancer Genetics. Thanks for all the laughs, the fun, and the “drinks” we shared. Special thanks go to Hege Kilen Andersen, Kristin Andersen, Lene Elisabeth Johannesen, and Laila Bergly for their contributions in my research projects. Infine voglio ringraziare i miei genitori, la mia famiglia e tutti i miei amici per avermi supportato ed incoraggiato in tutti questi anni lontano da casa. Oslo, February 2018 4 List of Papers Paper I: A novel truncated form of HMGA2 in tumors of the ovaries Agostini A, Panagopoulos I, Davidson B, Tropé CG, Heim S, Micci F. Oncology Letters 2016 Aug;12(2):1559-1563 Paper II: Genomic imbalances are involved in miR-30c and let-7a deregulation in ovarian tumors: implications for HMGA2 expression Agostini A, Brunetti M, Davidson B, Tropé CG, Heim S, Panagopoulos I, Micci F. Oncotarget 2017 Mar 28;8(13):21554-21560 Paper III: The microRNA mir-192/215 family is upregulated in mucinous ovarian carcinomas Agostini A, Brunetti M, Davidson B, Tropé CG, Heim S, Panagopoulos I, Micci F. Submitted manuscript (Scientific Reports) Paper IV: Recurrent involvement of DPP9 in gene fusions in serous ovarian carcinoma Smebye ML, Agostini A, Johannessen B, Thorsen J, Davidson B, Tropé CG, Heim S, Skotheim RI, Micci F. BMC Cancer 2017 Sep 11;17(1):642 Paper V: Identification of novel cyclin gene fusion transcripts in endometrioid ovarian carcinomas Agostini A, Brunetti M, Davidson B, Tropé CG, Heim S, Panagopoulos I, Micci F. Submitted manuscript (International Journal of Cancer) 6 “Science, my lad, is made of mistakes, but they are mistakes which are useful to make, because they lead little by little to the truth” ― Jules Verne, A Journey to the Center of the Earth 7 Table of contents List of Papers.............................................................................................................................. 6 Part 1: Introduction................................................................................................................... 11 Ovarian tumors..................................................................................................................... 11 Epithelial tumors............................................................................................................... 12 Borderline epithelial tumors......................................................................................... 12 Ovarian carcinomas...................................................................................................... 13 Sex cord-stromal tumors ................................................................................................... 14 Pure stromal tumors ..................................................................................................... 14 Pure sex cord tumors .................................................................................................... 14 The hallmarks of cancer ....................................................................................................... 16 Genomic instability .............................................................................................................. 18 Chromosomal instability ...................................................................................................... 19 Fusion genes......................................................................................................................... 21 Clinical relevance of fusion genes in solid tumors ........................................................... 24 Somatic point mutations in cancer ....................................................................................... 25 Genomic alterations and mutations in ovarian tumors......................................................... 26 Fusion genes in ovarian carcinomas ................................................................................. 28 microRNAs: biogenesis and main functions........................................................................ 29 miRNAs and cancer ............................................................................................................. 32 Clinical relevance......................................................................................................... 35 miRNAs in ovarian cancer ................................................................................................... 36 High-mobility group AT-hook 2 (HMGA2)......................................................................... 38 HMGA2 regulation............................................................................................................ 39 HMGA2 role in cancer...................................................................................................... 42 Part 2: Materials and methods.................................................................................................. 44 Patient material..................................................................................................................... 44 Methods................................................................................................................................ 45 Cancer cytogenetics .......................................................................................................... 45 Short-term cultures and karyotyping of solid tumors................................................... 46 Fluorescence in situ hybridization (FISH) ................................................................... 46 Comparative genomic hybridization (CGH) ................................................................ 47 8 Polymerase chain reaction (PCR) based techniques: brief history of a “special” DNA polymerase ......................................................................................................................
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