Clinical Epigenetics (eBook)

Preface 5
Epigenetics: A Lay Description 6
Epigenetics: A Scientific Description 7
Contents 9
About the Editors 10
1: Genetics and Epigenetics: A Historical Overview 11
1.1 The Early Origins of Genetics 11
1.2 Discovery of DNA 13
1.3 Early Characterisation of DNA 13
1.4 Discovering That Genes Are Made of DNA 14
1.5 The Birth and Evolution of Epigenetics 16
1.6 The Double Helix Structure of DNA 17
1.7 The Discovery of DNA Methylation 18
1.8 The X-Chromosome and Its Unique Place in Genetics and Epigenetics 19
1.9 Heritability of DNA Methylation 25
1.10 Genomic Imprinting 26
1.11 Why Do Genes Become Imprinted? 28
1.12 How Do Genes Become Imprinted? 29
1.13 Histones, Nucleosomes and Chromatin Structure 30
1.14 Cancer Epigenetics 33
1.15 A Molecular Definition of the Term `Gene´ 34
1.16 CpG Islands 36
1.17 How Does DNA Methylation Cause Transcriptional Silencing? 38
1.18 Epigenomics 38
1.19 Key Milestones in Genetics and Epigenetics 41
1.20 Key Discoveries 43
References 50
2: The DNA Methylation Machinery 57
2.1 DNA Methylation/Methylcytosine 57
2.2 Readers of Methylcytosine: DNA Methylation and Gene Expression 60
2.2.1 Methyl-CpG-Binding Domain Proteins (MBD) 61
2.3 Writers of Methylcytosine: DNA Methyltransferases (DNMTs) 62
2.3.1 The Function of DNMTs: Maintenance Methylation 63
2.3.2 The Function of DNMTs: Establishment of DNA Methylation 64
2.3.3 CpG Islands 65
2.4 Erasers of Methylcytosine 65
2.4.1 Regulation of DNA Demethylation by TET Enzymes 66
2.5 Conclusion 67
References 67
3: 5-Methylcytosine and Its Oxidized Derivatives 75
3.1 Introduction 75
3.2 DNA Methyltransferases 78
3.3 The Function of 5-Methylcytosine 78
3.4 Mutations in DNMT1 81
3.5 Mutations in DNMT3A 81
3.6 Mutations in DNMT3B 82
3.7 5-Methylcytosine-Binding Proteins 82
3.8 5-Methylcytosine Oxidases, the TET Proteins 84
3.9 Biological Role of 5-Hydroxymethylcytosine in Development and Disease 85
3.10 Mutations in TET2 86
3.11 Proteins That Bind to Oxidized 5-Methylcytosine Derivatives 87
References 88
4: The Role of Nucleosomes in Epigenetic Gene Regulation 97
4.1 Introduction 98
4.2 The Role of the Nucleosome 98
4.2.1 Nucleosome Remodelling 100
4.2.2 Variant Nucleosomes 101
4.3 Histone Post-Translational Modifications 101
4.3.1 Histone Acetylation 102
4.3.2 Histone Methylation 104
4.4 DNA Methylation 105
4.5 Transcription Regulation 105
4.5.1 Promoters 105
4.5.1.1 Histone Modifications at Promoters 106
4.5.1.2 Histone Variants at Promoters 107
4.5.1.3 Nucleosome Positioning at Promoters 108
4.5.1.4 DNA Methylation at Promoters 108
4.5.1.5 Promoter Nucleosomes and Cancer 109
4.5.2 Enhancers 109
4.5.2.1 Histone Modifications at Enhancers 110
4.5.2.2 Nucleosome Positioning at Enhancers 110
4.5.2.3 DNA Methylation at Enhancers 111
4.5.3 Gene Bodies 111
4.5.3.1 Histone Modifications at Gene Bodies 111
4.5.3.2 Nucleosome Positioning at Gene Bodies 112
4.5.3.3 DNA Methylation at Gene Bodies 112
4.5.4 Bivalent Chromatin 113
4.5.4.1 Bivalent Promoters 113
4.5.4.2 Bivalent Enhancers 114
4.5.5 Nucleosome Asymmetry 114
4.6 Future Directions 115
4.7 Concluding Remarks 116
References 116
5: Circular RNAs in Human Health and Disease 128
5.1 Introduction 128
5.2 Types of RNA 129
5.2.1 Circular RNAs 129
5.3 Circular RNAs in Human Disease 130
5.4 Linear RNA-seq 130
5.4.1 Library Preparation 131
5.4.2 Sequencing 131
5.4.3 Data Analysis 132
5.5 CircRNA Detection Tools, Challenges and Solutions 132
5.6 Mechanisms of CircRNA Action 134
5.7 Current Understanding of CircRNAs as Biomarkers 135
5.8 Future Requirements 137
References 138
6: The Role of Histone Variants in Cancer 142
6.1 Nucleosome Organisation 143
6.2 Canonical and Variant Histones 144
6.2.1 Histone Chaperones 144
6.2.2 Nomenclature of Histone Variants 144
6.2.3 Histone Variants of H2A 145
6.2.3.1 Function of H2A Histone Variants 145
H2A.X 145
H2A.Z.1, H2A.Z.2.1 and H2A.Z.2.2 145
H2A.Bbd 148
macroH2A1.1, macroH2A1.2 and macroH2A2 148
6.2.4 Summary of Histone H2A Variants 149
6.2.5 Histone Variants of H2B 149
6.2.5.1 Function of H2B Histone Variants 149
6.2.6 Histone Variants of H3 149
6.2.6.1 Function of H3 Histone Variants 150
Replacement Histone Variants: H3.3, CENPA 150
Function of H3.4 151
Function of H3.5 151
Function of H3.Y.1 and H3.Y.2 151
6.3 Further Complexity of Variant Histone Chromatin Control 151
6.3.1 Heterotypic Nucleosomes and Homotypic Variant Nucleosomes 152
6.3.2 Post-translational Modifications 152
6.4 Histone Variants in Disease 153
6.4.1 Histone Variants in Cancer 153
6.4.1.1 H2A.Z.2 in Melanoma 153
6.4.1.2 CENPA in Cancer 153
6.4.1.3 Chaperone Proteins in Cancer 153
6.5 Conclusion 154
References 155
7: DNA Methylation and Carcinogenesis: Current and Future Perspectives 161
7.1 Epigenetic Alterations in Cancer 161
7.1.1 DNA Methylation 161
7.1.2 Hypomethylation 162
7.1.3 Hypermethylation 164
7.1.4 Somatic Mutations and DNA Methylation 166
7.1.5 Mutations in Methylation Modifiers 167
7.2 The Clinical Relevance of DNA Methylation in Cancer 167
7.2.1 Epigenetic Therapies 167
7.2.2 Reversibility of Aberrant DNA Methylation 168
7.2.3 Epigenetic Therapies as Useful Adjuncts to Traditional Therapies 169
7.2.4 Personalised Treatment Options 170
7.3 Clinical Implications of DNA Methylation in Cancer Prognosis 171
7.3.1 DNA Methylation as a Potential Biomarker in Cancer Diagnosis 171
7.3.2 Cancer Stratification and Treatment Implications 172
7.4 Future Perspectives of DNA Methylation in Cancer Treatment 174
References 175
8: Dysregulation of Cis-Regulatory Elements in Cancer 180
8.1 Introduction 181
8.2 Function of CREs and Dysregulation in Cancer 183
8.2.1 Accessibility to CREs 184
8.2.2 Promoters 184
8.2.3 Enhancers and Super-Enhancers 185
8.2.4 Silencers and Insulators 185
8.3 Acquisition of Somatic Mutations and Structural Variants in Cancer Genomes 186
8.4 Somatic Alterations to Cis-Regulatory Regions in Cancer 188
8.4.1 Large Surveys of Non-coding Cancer Mutations Reveal Frequent Mutations in CREs 188
8.4.2 Mutations in Promoter Elements and Transcription Factor Binding Sites that Are Important in Cancer 190
8.4.3 Somatic Alterations Can Create and Remodel Enhancers and Super-Enhancers by `Enhancer Hijacking´ to Drive Oncogene Expre... 191
8.4.4 Somatic Disruption of the Silencer CTCF and Insulators Is a Frequent Event in Cancer 192
8.5 Clinical Uses of Somatic Alterations to CREs in Cancer 193
8.6 Conclusion 194
References 194
9: Germline Epigenetic Testing of Imprinting Disorders in a Diagnostic Setting 200
9.1 Introduction 201
9.2 Genomic Imprinting 201
9.3 Human Imprinting Disorders 203
9.4 Methods to Detect Germline Methylation Abnormalities in a Clinical Setting 209
9.4.1 Methylation-Sensitive Multiplex Ligation-Dependent Probe Amplification (MS-MLPA) 209
9.4.2 Methylation-Sensitive High-Resolution Melting Analysis 214
9.4.3 Taqman Allele-Specific Methylated Multiplex Quantitative PCR 215
9.4.4 Bisulphite Pyrosequencing 215
9.4.5 Methylation Arrays and Genome-Wide Methods 216
9.4.6 Next-Generation Sequencing 217
9.5 Summary and Concluding Remarks 218
References 218
10: Cancer Methylation Biomarkers in Circulating Cell-Free DNA 223
10.1 Introduction 224
10.2 DNA Methylation Biomarkers 226
10.3 Methylated DNA Blood-Based Biomarkers 227
10.3.1 Colorectal Cancer 227
10.3.2 Breast Cancer 228
10.3.3 Prostate Cancer 229
10.3.4 Ovarian Cancer 230
10.3.5 Lung Cancer 231
10.3.6 Brain Cancer 233
10.3.7 Pancreatic Cancer 235
10.4 Cancer Tissue-of-Origin Detection Using cfDNA Methylation Biomarkers 238
10.5 Analytical Methods for Detecting Methylated ctDNA 239
10.6 Clinical Utility of Methylated ctDNA 240
10.7 Methylated cfDNA Biomarkers Currently in the Clinic 242
10.8 Challenges and Limitations 242
10.9 Future Perspectives 243
References 244
11: The Clinical Utility of Epigenetics: A Case Study 252
11.1 Introduction 252
11.2 Clinical Background 253
11.3 Results of Genetic Testing 258
11.4 Laboratory Tests Performed to Determine the Presence or Absence of a Constitutional Epimutation 258
11.5 Results of Testing to Determine the Presence or Absence of a Constitutional Epimutation and Interpretation 259
11.6 Comments 262
11.7 Answers to the Questions Embedded in the Text 264
References 269