Durham E-Theses The Transcriptomic and Genomic Analysis of Lamin A/C Expression in the Colon and in Colorectal Cancer RAHMAN-CASANS, SYED,FIDA,UR How to cite: RAHMAN-CASANS, SYED,FIDA,UR (2011) The Transcriptomic and Genomic Analysis of Lamin A/C Expression in the Colon and in Colorectal Cancer, Durham theses, Durham University. Available at Durham E-Theses Online: http://etheses.dur.ac.uk/3460/ Use policy The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in Durham E-Theses • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full Durham E-Theses policy for further details. Academic Support Oce, Durham University, University Oce, Old Elvet, Durham DH1 3HP e-mail: [email protected] Tel: +44 0191 334 6107 http://etheses.dur.ac.uk 2 The Transcriptomic and Genomic Analysis of Lamin A/C Expression in the Colon and in Colorectal Cancer by Syed Fida-ur Rahman-Casañs A thesis submitted to University of Durham in fulfilment of the requirements for the degree of Doctor of Philosophy (Ph.D) University of Durham School of Biological and Biomedical Sciences August 2011 1 | P a g e Contents The Transcriptomic and Genomic Analysis of Lamin A/C Expression in the Colon and in Colorectal Cancer ............................................................................................... 1 CONTENTS.................................................................................................................................... 2 ACKNOWLEDGEMENTS .............................................................................................................. 8 DECLARATION ............................................................................................................................10 ABSTRACT ....................................................................................................................................11 ABBREVIATIONS ........................................................................................................................13 CHAPTER 1 ...................................................................................................................................24 INTRODUCTION..........................................................................................................................24 1.1 Cancer of the colon and rectum Epidemiology ................................................... 24 Figure 1.1 ........................................................................................................... 25 Figure 1.2 ........................................................................................................... 25 Figure 1.3 ........................................................................................................... 26 1.1.1 Staging of Colon and Rectal Cancer ................................................... 26 Figure 1.4 ........................................................................................................... 27 Figure 1.5 ........................................................................................................... 28 Table 1.1 ............................................................................................................ 29 Table 1.2 ............................................................................................................ 29 Table 1.3 ............................................................................................................ 29 1.1.2 Detection and Screening for Bowel cancer ......................................... 30 1.1.3 Treatment of Bowel Cancer ................................................................ 31 1.1.4 Prognostic Factors in Bowel Cancer ................................................... 32 1.1.5 Molecular Markers .............................................................................. 34 1.2 Development and Structure of the Colon and Rectum ....................................... 37 1.2.1 Embryological Development ............................................................... 37 1.2.2 Anatomical Layers .............................................................................. 38 Figure 1.6 ........................................................................................................... 38 1.2.3 Physiological Function ........................................................................ 39 1.2.4 The Colon Crypt as a Functional Unit and its Genetic Regulation ....... 40 Figure 1.7 ........................................................................................................... 41 2 | P a g e Figure 1.9 ........................................................................................................... 42 1.3 Colorectal Carcinogenesis – A Multistep Phenomenon ...................................... 44 Figure 1.10 ......................................................................................................... 45 1.3.1 Aberrant Crypt Foci (ACF) .................................................................. 45 1.3.2 Early Adenomas – Role of APC (5q21) ............................................... 46 1.3.3 Intermediate Adenomas – Proto-oncogene mutations ........................ 47 1.3.4 Late Adenomas – Mutations in tumour suppressor genes .................. 47 Figure 1.11 ......................................................................................................... 49 1.4 Sporadic and Inherited Bowel Cancer types ....................................................... 50 1.4.1 Sporadic Cancer ................................................................................. 50 Figure 1.12 ......................................................................................................... 50 1.4.2 Inherited bowel cancer syndromes ..................................................... 51 1.5 The Mammalian Nucleus ....................................................................................... 53 1.5.1 The Nuclear Envelope and its Dynamic Function ................................ 53 1.5.2 The Cell Cycle ........................................................................................... 55 Figure 1.14 ......................................................................................................... 56 Figure 1.15 ......................................................................................................... 57 1.5.2 The Nuclear Lamina ........................................................................... 59 Figure 1.16 ......................................................................................................... 60 Figure 1.17 ......................................................................................................... 62 Table 1.4 ............................................................................................................ 62 Figure 1.18 ......................................................................................................... 63 Figure 1.19 ......................................................................................................... 66 1.5.3 Laminopathies .................................................................................... 68 1.5.4 Lamins and Cancer ............................................................................ 74 1.6 Stem cells ................................................................................................................. 74 1.7 Thesis aims .............................................................................................................. 78 CHAPTER 2 ...................................................................................................................................80 MATERIALS AND METHODS ...................................................................................................80 2.1 General Materials and Reagents / Chemicals ...................................................... 80 2.2 Patient Selection and Tissue Sampling ................................................................. 80 2.2.1 Patient selection .................................................................................. 80 2.2.2 Tissue samples for immunohistochemical analysis ............................. 80 2.2.3 Tissue samples for RNA analysis ....................................................... 81 2.2.4 Tissue samples for cryosectioning ...................................................... 81 2.3 Immunohistochemistry .......................................................................................... 82 2.3.1 Colonic tissue samples ........................................................................ 82 2.3.2 Antigen retrieval ................................................................................... 82 3 | P a g e 2.3.3 Peroxidase staining reaction ................................................................ 82 Table 2.1 ............................................................................................................ 83 2.3.4 Counterstaining ................................................................................... 84 2.3.5 Image analysis....................................................................................