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Identification of Cancer-Specific Transcripts Identification of cancer-specific transcripts: With emphasis on the hunt for fusion genes in colorectal cancer Marthe Eken Thesis for the master’s degree in Molecular Bioscience at Department of Molecular Bioscience (IMBV), Faculty of Mathematics and Natural sciences UNIVERSITY OF OSLO December 2008 2 Acknowledgements This work was carried out in the project Group of Genome Biology, at the Department of Cancer Prevention, Rikshospitalet-Radiumhospitalet Medical Center, from March 2007 to December 2008. First of all, I would like to thank my supervisor, Rolf I. Skotheim, for his great support throughout the project, for always taking the time to answer my many questions, and for his everlasting patience with my forgotten italics. I also wish to thank my co-supervisor and head of the department, Ragnhild A. Lothe, for giving me the opportunity to be part of such an excellent group. I greatly appreciate the other members of the department for making this a great place to work, especially Guro for being my lab-oracle, Anita for providing microarray data, Zere for helping me with the cloning, and Hilde for our many discussions. I am grateful to my mother for all her great advices through the years and for always being there for me, and to my father for telling me I could do anything. Finally, special thanks go to my fiancé, Joachim, for his overwhelming patience and support, for always believing in me, and for making me believe in myself. Oslo, December 2008 Marthe Eken Table of contents TABLE OF CONTENTS..................................................................................................................... 4 SUMMARY .......................................................................................................................................... 6 ABBREVIATIONS .............................................................................................................................. 8 GENE SYMBOLS ................................................................................................................................ 9 1. INTRODUCTION ................................................................................................................... 10 1.1 THE MOLECULAR PHENOTYPE OF CANCER ............................................................................. 10 1.2 TRANSCRIPT VARIATION IN CANCER ...................................................................................... 11 1.2.1 Alternative splicing .................................................................................................... 12 1.2.2 Alternative core promoter usage ................................................................................ 15 1.3 FUSION GENES IN CANCER ..................................................................................................... 16 1.3.1 Chromosomal rearrangements ................................................................................... 16 1.3.2 Creation of fusion genes from chromosomal rearrangements ................................... 19 1.3.3 Discovery and detection of fusion genes .................................................................... 21 1.3.4 Fusion gene targeting therapy ................................................................................... 22 1.4 COLORECTAL CANCER ........................................................................................................... 23 1.4.1 Developmental pathways ........................................................................................... 24 1.4.2 Dukes' staging, current treatment and outcome ........................................................ 25 1.5 OTHER CANCER DISEASES STUDIED ....................................................................................... 27 1.5.1 Malignant peripheral nerve sheath tumour ............................................................... 27 1.5.2 Leukaemia .................................................................................................................. 28 1.5.3 Testicular germ cell tumour ....................................................................................... 28 2. AIMS ......................................................................................................................................... 30 3. MATERIALS AND METHODS ............................................................................................ 31 3.1 MATERIALS ........................................................................................................................... 31 3.1.1 Cancer cell lines – colon cancer, testicular cancer, and leukaemia .......................... 31 3.1.2 Tissue samples – malignant peripheral nerve sheath tumours and colorectal carcinomas ................................................................................................................ 31 3.2 PUBLICLY AVAILABLE DATABASES ........................................................................................ 32 3.3 ESTABLISHMENT OF METHODOLOGICAL PROTOCOLS IN EXISTING PROJECTS ......................... 32 3.3.1 Analysis of BIRC5 transcipt variants in MPNST samples ......................................... 32 3.3.2 Validation of fusion gene microarray data ................................................................ 33 3.3.3 Analysis of putative fusion genes in a testicular cancer cell line ............................... 35 3.4 DESIGN OF A NOVEL STRATEGY FOR IDENTIFICATION OF FUSION GENES ................................ 36 4 3.4.1 Outlier expression profiles .......................................................................................... 36 3.4.2 Known and putative 3’ fusion gene partners .............................................................. 38 3.4.3 Exon microarray analysis ........................................................................................... 39 3.5 EXPERIMENTAL ASSAYS ......................................................................................................... 42 3.5.1 Polymerase chain reaction ......................................................................................... 42 3.5.2 Rapid Amplification of cDNA Ends ............................................................................ 44 3.5.3 Detection of PCR-products ......................................................................................... 47 3.5.4 Cloning........................................................................................................................ 48 3.5.5 DNA Sequencing ......................................................................................................... 50 4. RESULTS .................................................................................................................................. 52 4.1 BIRC5 TRANSCRIPT VARIANTS ............................................................................................... 52 4.2 FUSION GENE MICROARRAY ................................................................................................... 52 4.3 PUTATIVE FUSION GENES IN TGCT ........................................................................................ 53 4.4 NOVEL STRATEGY FOR IDENTIFICATION OF FUSION GENES ..................................................... 54 5. DISCUSSION ........................................................................................................................... 73 5.1 SPLICE VARIANTS OF BIRC5 IN CANCER ................................................................................. 73 5.2 VALIDATION OF A NOVEL MICROARRAY-BASED TOOL ............................................................ 74 5.3 PUTATIVE FUSION GENES IN TGCT ........................................................................................ 75 5.4 HUNT FOR FUSION GENES ....................................................................................................... 76 5.4.1 Methodological considerations ................................................................................... 76 5.4.2 Novel exons and transcripts ........................................................................................ 78 6. FUTURE PERSPECTIVES .................................................................................................... 85 7. REFERENCE LIST ................................................................................................................. 86 APPENDIX I – PRIMER INFORMATION .................................................................................... 98 APPENDIX II – RESULTS ............................................................................................................. 101 APPENDIX III – KNOWN FUSION GENES IN CANCER ........................................................ 110 APPENDIX IV – ABSTRACTS OF MANUSCRIPTS ................................................................. 118 5 Summary Cancer is a genetic and epigenetic disease where accumulation of alterations in the genome and epigenome of a cell eventually leads to malignancy. Detection and diagnosis of cancer are nevertheless not trivial issues, and furthermore, drugs intended to kill the cancer cells may as well exert their effects on normal cells. This may be due to the lack of specificity of the drugs toward their intended targets, or a lack of cancer-specificity of the drug targets themselves. Events like alternative splicing and chromosomal rearrangements can create cancer-specific transcripts, which themselves or their derived protein products can be considered
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