Novel genetic and epigenetic alterations in colorectal tumors and their potential as biomarkers Terje Cruickshank Ahlquist Group of Molecular Genetics Department of Cancer Prevention Institute for Cancer Research The Norwegian Radium Hospital Rikshospitalet University Hospital Faculty Division The Norwegian Radium Hospital Faculty of Medicine University of Oslo The Research Council of Norway Norwegian Centre of Excellence University of Oslo A thesis for the PhD degree, Oslo, 2008 © Terje Cruickshank Ahlquist, 2009 Series of dissertations submitted to the Faculty of Medicine, University of Oslo No. 766 ISBN 978-82-8072-325-3 All rights reserved. No part of this publication may be reproduced or transmitted, in any form or by any means, without permission. Cover: Inger Sandved Anfinsen. Printed in Norway: AiT e-dit AS, Oslo, 2009. Produced in co-operation with Unipub AS. The thesis is produced by Unipub AS merely in connection with the thesis defence. Kindly direct all inquiries regarding the thesis to the copyright holder or the unit which grants the doctorate. Unipub AS is owned by The University Foundation for Student Life (SiO) TABLE OF CONTENTS ACKNOWLEDGEMENTS .............................................................................................................5 PREFACE.............................................................................................................................................6 LIST OF PAPERS...............................................................................................................................8 SUMMARY...........................................................................................................................................9 GENERAL INTRODUCTION ....................................................................................................11 Genetic and epigenetic inheritance .............................................................................................11 Cancer as a genetic and epigenetic disease.................................................................................12 DNA mutations in cancer ............................................................................................................13 DNA methylation..........................................................................................................................15 DNA methylation and cancer .................................................................................................20 Colorectal cancer ...........................................................................................................................21 Incidence, treatment and outcome – Nature versus Nurture.............................................21 Genetics and epigenetics of CRC – a timeline......................................................................24 Molecular and morphological developmental pathways in colorectal cancer..................25 Instabilities involved in colorectal cancer..............................................................................28 Chromosomal instability – CIN.........................................................................................28 Microsatellite instability – MSI...........................................................................................28 CpG island methylator phenotype – CIMP......................................................................30 Signaling pathways ....................................................................................................................32 Clinical challenges for CRC.....................................................................................................33 AIMS....................................................................................................................................................37 RESULTS IN BRIEF .......................................................................................................................38 DISCUSSION....................................................................................................................................43 Fresh-frozen versus formalin embedded tissue....................................................................43 Methodological considerations....................................................................................................43 DNA methylation analyses......................................................................................................43 Bisulfite treatment ................................................................................................................43 Methylation specific PCR (MSP)........................................................................................44 Scoring of MSP results ........................................................................................................45 Bisulfite sequencing..............................................................................................................46 Mutation analyses......................................................................................................................47 Denaturing high performance liquid chromatography ...................................................48 Direct sequencing.................................................................................................................50 Fragment analysis .................................................................................................................51 Multiplex-dependent probe amplification ........................................................................52 Clinical impact of molecular biology ..........................................................................................54 Early tumor markers.................................................................................................................54 Prognostic markers ...................................................................................................................56 Predictive markers.....................................................................................................................58 Survival analyses........................................................................................................................60 Driver and passenger (epi)mutations..........................................................................................61 Different origins of colorectal cancer contribute to a non-uniform disease ........................63 CONCLUSIONS...............................................................................................................................64 Introduction FUTURE PERSPECTIVES............................................................................................................65 REFERENCES..................................................................................................................................68 ORIGINAL ARTICLES...................................................................................................................... APPENDIX............................................................................................................................................ Appendix I. Associated paper.......................................................................................................... Appendix II. Abbreviations ............................................................................................................. ACKNOWLEDGEMENTS The present work has been performed at the Department of Cancer Prevention, Institute for Cancer Research at Rikshospitalet University Hospital – Radiumhospitalet and was supported by the Research Council of Norway and Centre for Cancer Biomedicine. I am grateful for working under my supervisor, Professor Ragnhild Lothe, who with her supreme knowledge, enthusiasm and kindness has made it easy to thrive both scientifically and socially. Especially big thanks to post doc Guro Lind for being invaluable, both by helping out in the lab as well as with preparing manuscripts. A big “grazie” to Professor Bruno Dallapiccola for inviting me to his excellent research facilities in Rome to work, and also to Irene Bottillo who with her excellent laboratory skills and including, friendly nature made my stay scientifically as well as socially very rewarding. A big thanks goes to co-authors and collaborators for very good biological material, clinical data and scientific input. I would also like to acknowledge Professor Arild Nesbakken for being my official link to the Faculty of Medicine, as well as contributing with valuable feedback on the clinical aspects of the thesis. Kudos to all my good friends and colleagues in the department who have meant the world to me. Special thanks to Helge and Marianne for making my day as we’ve been my office mates for 5 years. An important factor in completing this thesis is the personnel the Narvesen kiosk who ensured that my blood-sugar was at a constantly elevated level. Jan-Ivar Hansen, my biology teacher at Bjørknes Privatskole was so in love with biology that it was impossible not to be the same. Thanks! This thesis had never even been started if it wasn’t for my wonderful wife, Hege and my parents. Her for making me not want to study medicine in Hungary, and them for teaching me to have high standards and big aims. I love you! Oslo, December 23rd 2008 PREFACE “Is it just me? Or does everyone come across genetics, genes, and DNA almost everywhere?”