Novel genetic and epigenetic alterations in ... - Ous-research.no

TABLE OF CONTENTSACKNOWLEDGEMENTS .............................................................................................................5PREFACE.............................................................................................................................................6LIST OF PAPERS...............................................................................................................................8SUMMARY...........................................................................................................................................9GENERAL INTRODUCTION ....................................................................................................11Genetic and epigenetic inheritance .............................................................................................11Cancer as a genetic and epigenetic disease.................................................................................12DNA mutations in cancer ............................................................................................................13DNA methylation..........................................................................................................................15DNA methylation and cancer .................................................................................................20Colorectal cancer ...........................................................................................................................21Incidence, treatment and outcome – Nature versus Nurture.............................................21Genetics and epigenetics of CRC – a timeline......................................................................24Molecular and morphological developmental pathways in colorectal cancer ..................25Instabilities involved in colorectal cancer..............................................................................28Chromosomal instability – CIN.........................................................................................28Microsatellite instability – MSI ...........................................................................................28CpG island methylator phenotype – CIMP......................................................................30Signaling pathways ....................................................................................................................32Clinical challenges for CRC.....................................................................................................33AIMS....................................................................................................................................................37RESULTS IN BRIEF .......................................................................................................................38DISCUSSION....................................................................................................................................43Fresh-frozen versus formalin embedded tissue....................................................................43Methodological considerations....................................................................................................43DNA methylation analyses......................................................................................................43Bisulfite treatment ................................................................................................................43Methylation specific PCR (MSP)........................................................................................44Scoring of MSP results ........................................................................................................45Bisulfite sequencing..............................................................................................................46Mutation analyses......................................................................................................................47Denaturing high performance liquid chromatography ...................................................48Direct sequencing.................................................................................................................50Fragment analysis .................................................................................................................51Multiplex-dependent probe amplification ........................................................................52Clinical impact of molecular biology ..........................................................................................54Early tumor markers.................................................................................................................54Prognostic markers ...................................................................................................................56Predictive markers.....................................................................................................................58Survival analyses........................................................................................................................60Driver and passenger (epi)mutations..........................................................................................61Different origins of colorectal cancer contribute to a non-uniform disease ........................63CONCLUSIONS...............................................................................................................................64