Biomarkers and Risk Stratification in Colorectal Neoplasia A thesis submitted to the University of Manchester for the degree of Doctor of Medicine in the Faculty of Biology, Medicine and Health. 2019 Lyndsay E Pearce BMedSci BMBS FRCS School of Medical Sciences Table of Contents 1 Introduction ................................................................ 18 1.1 Pre symptomatic diagnosis and screening for Colorectal Cancer ............................................................................. 21 1.1.1 Background to Colorectal Cancer Screening ............................... 21 1.1.2 The UK National Bowel Cancer Screening Programme .................. 23 1.1.3 Faecal Occult Blood Testing ..................................................... 23 1.1.4 Faecal immunohistochemical testing ......................................... 24 1.1.5 Flexible sigmoidoscopy ........................................................... 25 1.1.6 Individualising risk and colorectal cancer screening .................... 26 1.1.7 Moderate Familial Risk ........................................................... 26 1.1.8 Screening in familial colorectal cancer syndromes ...................... 27 1.2 Single Gene disorders .................................................... 29 1.2.1 Familial Adenomatous Polyposis .............................................. 29 1.2.1.1 Introduction and History ................................................... 29 1.2.1.2 Variation in phenotypic features ......................................... 30 1.2.1.3 Desmoid Tumours ............................................................ 31 1.2.1.4 Polyp surveillance in FAP and AFAP .................................... 32 1.2.2 Lynch Syndrome ................................................................... 33 1.2.1.1 Introduction and History ................................................... 33 1.2.1.2 Diagnosis of Lynch Syndrome ............................................ 34 1.2.1.3 Amsterdam/Bethesda Criteria ............................................ 37 1.2.1.4 Other predictive models .................................................... 40 1.2.1.5 Genetic modifiers ............................................................. 41 1.2.1.6 Surveillance and screening in Lynch Syndrome .................... 42 1.2.3 Polyposis Phenotype .............................................................. 45 1.2.3.1 Hyperplastic Polyposis ...................................................... 45 1.2.3.2 Multiple Adenoma Phenotype ............................................. 46 1.2.3.2.1 Oligopolyposis .......................................................... 46 1.2.3.2.2 MUTYH associate polyposis ........................................ 47 1.2.3.2.3 NTHL1-associated polyposis ....................................... 48 1.2.3.3 Peutz Jeghers Syndrome ................................................... 48 1.2.3.4 Juvenile Polyposis Syndrome ............................................. 48 1.2.3.5 Cowden’s Syndrome ......................................................... 49 1.3 Diagnosis and Staging of Colorectal Cancer .................. 50 1.3.1 Imaging and diagnosis of CRC ................................................. 50 1.3.2. Pathology of Colorectal Cancer ................................................. 53 1.3.2.1 Adenocarcinoma .............................................................. 53 1.3.2.2 Precursor lesions (polyps) ................................................. 53 1.3.2.2.1 Adenomas ............................................................... 53 1.3.2.2.2 Serrated Adenomas .................................................. 54 1.3.2.2.3 Hamartomas ............................................................ 55 1.3.2.2.4 Inflammatory Polyps ................................................. 56 1.3.3 Staging of colorectal cancer .................................................... 56 1.3.3.1 Radiological staging ......................................................... 57 1.3.3.1.1. PET CT .................................................................... 58 1.4 Treatment of Colorectal Cancer ...................................... 58 1.4.1. Early colorectal cancer ............................................................ 58 1.4.2 Stage II , III and IV Colorectal cancer ...................................... 58 1.4.3 Treatment considerations in Lynch Syndrome ............................ 59 1.4.3.1 Prophylactic Surgery ........................................................ 60 1.4.3.2 Adjuvant Therapy ............................................................ 61 1.4.3.2.1 Fluorouracil-based adjuvant chemotherapy .................. 62 2 1.5 Follow-up after resection for Colorectal Cancer ............. 64 1.5.1 Carcinoembryonic Antigen ............................................... 64 1.5.2 CT scanning ................................................................... 65 1.5.3 Positron Emission Tomography (PET CT) ............................ 65 1.5.4 Surveillance programmes ................................................ 66 1.5.5 Colorectal liver metastases .............................................. 68 1.6 Colorectal Cancer Molecular Genetics ............................ 69 1.6.1 Fearon and Vogelstein’s genetic model for tumourigenesis .... 70 1.6.2 Jass’ molecular classification of colorectal cancer ................. 70 1.6.3 Genetic Instability ............................................................ 71 1.6.3.1 Epigenetics ..................................................................... 71 1.6.3.2 Jass’ Classification ........................................................... 72 1.6.3.2.1 The Microsatellite Instability Pathway .......................... 73 1.6.3.2.2 The Chromosomal Instability Pathway ......................... 73 1.7 Principles of Biomarkers ............................................... 74 1.7.1 Categorisation of Biomarkers .................................................. 75 1.7.2 Biomarker Discovery .............................................................. 76 1.7.3 Biomarker Validation ............................................................. 77 1.7.4 Biomarker discovery roadmaps ............................................... 77 1.7.5 Biomarkers in Colorectal Cancer .............................................. 77 1.7.5.1 Risk stratification (predisposition) biomarkers ...................... 78 1.7.5.2 Screening and early detection biomarkers ........................... 78 1.7.5.3 Diagnostic Biomarkers ...................................................... 79 1.7.5.4 Pharmacological Biomarkers .............................................. 79 1.7.5.5 Predictive Biomarkers ....................................................... 79 1.7.5.5.1 KRAS ..................................................................... 80 1.7.5.6 Population based screening biomarkers .............................. 81 1.7.5.7 Predictive value of MSI in chemotherapy ............................. 81 1.7.5.8 Circulating Tumour Cells ................................................... 82 1.7.5.9 Tumour biology ............................................................... 83 1.7.5.9.1 Beta-2 microglobulin as a biomarker in MMR-deficient CRC 84 1.7.5.9.2 Immune response to tumour cells ............................... 85 1.7.5.9.3 Natural Killer Cells .................................................... 87 1.8 Common genetic variants and Colorectal Cancer ............ 88 1.8.1 Genome Wide Association Studies ........................................... 88 1.8.2 Single Nucleotide Polymorphisms ............................................ 89 1.8.3 Polygenic risk ....................................................................... 89 1.8.4 Genetic Linkage analysis ........................................................ 90 1.8.4.1 Common Disease/Common Variant Hypothesis .................... 90 1.8.4.2 Linkage disequilibrium ...................................................... 91 1.8.4.3 Direct and Indirect Association .......................................... 91 1.8.5 GWAS and colorectal cancer ................................................... 92 1.8.5.1 History and Discovery of SNPs in colorectal cancer ............... 94 1.8.6 Functions of CRC association single nucleotide polymorphisms ..... 95 1.8.6.1 BMP ............................................................................... 95 1.8.6.2 TERC ............................................................................. 96 1.8.7 Population specific risk ........................................................... 96 1.8.7.1 CRC risk and SNPs in high risk populations .......................... 97 1.8.7.2 Lynch syndrome and susceptibility loci ............................... 98 1.8.8 SNPs and adenoma ................................................................ 99 1.8.8.1 Polyposis Phenotype ........................................................ 100 1.8.8.1.1 FAP ....................................................................... 100 1.8.8.1.2 Oligopolyposis ......................................................... 101 1.8.9 Patterns of disease and types of disease .................................. 102 3 1.8.9.1 Protective effects ............................................................ 103 1.8.9.2 Long term survival and early onset colorectal cancer ........... 104 STUDY ONE ..................................................................... 105 The effect of intensive CT scanning in surveillance to detect the recurrence of colorectal