Molecular Genetics of Liver Neoplasia (eBook)

Preface 5
Contents 6
Contributors 9
Part I Introduction 13
1 Biology of Hepatocellular Carcinoma: Past, Present 
14 
1 Historical Perspective 15
2 Current Standing 16
3 HCC Etiologies 17
4 HCC Diagnosis 18
5 HCC Metastasis 20
6 HCC Genetics 22
7 Future Perspectives 24
References 24
2 Overview of Cholangiocarcinoma and Evidence for a Primary Liver Carcinoma Spectrum 29
1 Introduction 29
2 Overview of Cholangiocarcinoma 30
3 Evidence that PLC Comprise a Spectrum of Closely Related Tumors 32
4 Conclusions 38
References 39
Part II Liver Cancer Development and Pathogenesis 44
3 Pathology of Hepatocellular Carcinoma 45
1 Introduction 45
2 Precursor Lesions of HCC 47
2.1 Dysplastic Nodule 47
2.1.1 Low-Grade DN 47
2.1.2 High-Grade DNs 47
3 Hepatocellular Carcinoma 49
3.1 Small HCC of the Early Stage 49
3.1.1 Small HCC of the Vaguely Nodular Type (Early HCC) 50
3.1.2 Small HCC of Distinctly Nodular Type 51
3.2 Evolution From Early to Advanced HCC 52
3.2.1 A ''Nodule-in-Nodule'' Appearance 53
3.2.2 Clonal Dedifferentiation of HCC Cells in a Single Tumor Nodule 54
References 54
Part III Genetics and Epidemiology of Liver Cancer 57
4 Epidemiology of Hepatocellular Carcinoma 58
1 Global Incidence of Hepatocellular Carcinoma 58
1.1 Overview 58
1.2 Race/Ethnicity 61
1.3 Gender 61
1.4 Age 61
1.5 Distribution of Risk Factors 62
1.5.1 HCC in the United States 62
2 Risk Factors of Hepatocellular Carcinoma 63
2.1 Hepatitis B Virus 63
2.2 Hepatitis C Virus 65
2.3 Alcohol 66
2.4 Aflatoxin 67
2.5 Non-alcoholic Fatty Liver Disease (NAFLD) and Non-alcoholic Steatohepatitis (NASH) 67
2.6 Diabetes 68
2.7 Obesity 69
2.8 Tobacco 72
2.9 Oral Contraceptives 72
2.10 Diet 72
2.10.1 Coffee Drinking 73
3 Genetic Epidemiology of HCC 74
References 76
5 Genetics and Epidemiology of Cholangiocarcinoma 81
1 Introduction 81
2 Epidemiology 82
3 Genetics 83
3.1 Mechanisms of Mutagenesis in CCA 83
3.1.1 iNOS 83
3.1.2 DNA Repair Genes 84
3.1.3 Epigenetic Changes by DNA Methylation 85
3.2 Gene Defects in CCA 89
3.2.1 Oncogenes 89
3.2.2 Tumor Suppressor Genes 91
3.2.3 Other Genes 95
3.3 Microarray Data 96
3.4 Micro-RNAs 97
3.5 Summary 98
References 99
Part IV Molecular Basis of Cancer Susceptibility 106
6 Signaling Pathways in Viral Related Pre-neoplastic Liver Disease and Hepatocellular Carcinoma 107
1 Introduction 107
2 MAPK/ERK Signaling Pathway 109
3 The WNT/-Catenin Signaling Pathway 114
4 Wnt3 is a Ligand for FZD7 and Activates the -Catenin Signaling Cascade in HCC 117
5 Expression Analysis of Wnt/FZD/-Catenin Signaling Components in HCC Tumors of Different Etiology 120
6 Constitutive Activation of the Wnt/-Catenin and IN/IGF-1/IRS-1/MAPK Signaling Pathway is Necessary and Sufficient to Transform the Mammalian Liver in the Absence of Genetic Mutations 121
References 127
7 Epigenetic Effects of Persistent Hepatitis C Virus Infection and Hepatocellular Carcinoma 132
1 Introduction 133
2 The HCV Lifecycle 133
3 HCV Infection and Hepatic Inflammation, Fibrosis and Cirrhosis 135
4 Transgenic Mouse Models of HCV-Associated HCC 136
5 HCV Protein Expression and Oxidative Stress 137
6 HCV and the Cell Cycle 137
7 HCV Infection and Cellular Apoptosis 138
8 Modulation of Tumor Suppressor Protein Functions by HCV Proteins 138
8.1 p53 Pathway 139
8.2 Rb Pathway 140
8.3 Wnt Pathway 140
9 HCV Interactions with Other Regulatory Host Proteins 141
9.1 ATM 141
9.2 DDX3 141
9.3 Disruption of Innate Immunity as a Route to Carcinogenesis 142
9.4 Modulation of Signal Transduction Pathways by HCV-Encoded Proteins 142
10 Summary 143
References 143
8 DNA Methylation Status in Chronic Liver Disease and Hepatocellular Carcinoma 149
1 Introduction 150
2 DNA Methylation Alterations During Multistage Hepatocarcinogenesis 150
3 Abnormalities of DNMTs During Hepatocarcinogenesis 153
3.1 Overexpression of DNMT1 153
3.2 Splicing Alteration of DNMT3b and DNA Hypomethylation in Pericentromeric Satellite Regions 153
4 Altered Expression of Methyl-CpG Binding Proteins (MBDs) 154
5 Genome-Wide DNA Methylation Analysis 155
5.1 DNA Methylation Alterations During Multistage Hepatocarcinogenesis Occur in a Genome-Wide Manner 155
5.2 Carcinogenetic Risk Estimation Based on DNA Methylation Profiles 156
5.3 Prognostication of Patients with HCCs Based on DNA Methylation Profiles 158
6 Perspective 159
References 159
Part V Animal Models 162
9 Transgenic and Knockout Mouse Models of Liver Cancer 163
1 Introduction 163
2 Genetically Engineered Mouse Models for the Study of Liver Cancer 165
2.1 Viral Models of HCC 165
2.2 Hepatitis B Virus 165
2.3 Hepatitis C Virus 166
3 Chronic Liver Injury Models 167
4 Mouse Models Recapitulating Molecular Alterations of Human Hepatocarcinogenesis 167
4.1 Disruption of Cell Cycle Regulation: p53, Rb, E2F1, and SV40 T Antigen 168
4.2 Telomere Disfunction 169
4.3 Transforming Growth Factor Alpha (TGF-) 169
4.4 Ras/Mitogen-Activated Protein Kinase (MAPK) 170
4.5 Epidermal Growth Factor (EGF) and Platelet-Derived Growth Factor (PDGF) 170
4.6 Akt/Mammalian Target of Rapamycin (mTOR) 171
4.7 Wnt/ ß 
171 
4.8 Janus Kinase-Signal Transducer and Activator of Transcription Factor (Jak/Stat) 172
4.9 Hippo/Warts 173
4.10 Transforming Growth Factor-ß (TGF-ß) 174
4.11 C-Met and Hepatocyte Growth Factor (HGF) 175
4.12 Nuclear Factor kB (NF-kB) and Inflammation-Associated Models 176
4.13 c-Myc and Tgf-Alpha 178
4.14 C-Myc and E2f1 178
5 Other Models 179
6 Evaluating Cooperation of Multiple Oncogenic Events in Liver Cancer by Hydrodynamic Gene Delivery 180
7 Comparative and Integrative Functional Genomics of HCC: MouseHuman Comparison 182
8 Conclusions 182
References 182
10 Mosaic Cancer Mouse Models and Functional Oncogenomics in Hepatocellular Carcinoma 189
1 Introduction 189
2 Cancer Mouse Models for HCC 190
3 Cross-Species Oncogenomic Comparison for Accelerated Cancer Gene Discovery 192
References 195
11 The Zebrafish Model for Liver Carcinogenesis 197
1 Zebrafish as an Experimental Model 198
2 Zebrafish Models for Human Diseases 199
3 Chemical Carcinogen-Induced Tumors in Zebrafish 199
4 Molecular Validation of the Zebrafish Cancer Model by Transcriptome Analysis 201
5 Genetic Approaches to Generate Tumor Models in Zebrafish 203
6 Generation of Transgenic Zebrafish Liver Cancer Models 206
6.1 Overexpression of c-Myc oncogene in Zebrafish liver 207
6.2 Overexpression of kras V12 Oncogene in Zebrafish Liver 208
6.3 Comparison of c-Mycand kras V12 Transgenic Zebrafish in Production of Liver Tumors 211
7 Prospects 212
References 214
Part VI Global Gene Expression Profiling of Human Liver Cancer 219
12 Integrative and Functional Genomics of HCC 220
1 Functional Genomics of HCC: Microarray-Based Technologies, and Gene Expression Profiling 221
1.1 Molecular Classification of Liver Cancer 222
1.2 Etiology-Associated Gene Expression Signatures 223
1.3 Gene Signatures for Recurrence and Metastasis 224
1.4 From Supervised to Unsupervised Approach: A Prediction Model for Survival 226
1.5 Gene Expression Profiling of Non-Coding Genes 227
2 Comparative Oncogenomics: Cross-species Comparison of Gene Expression Data 228
2.1 The Neutral Theory of Evolution as a Basis for Comparative Oncogenomics 228
2.2 Identification of Best-fit Mouse Models to Study Human HCC 229
2.3 A Novel HCC Subtype with Progenitor Cell Origin 230
2.4 Prognostication of Human HCC using Gene Signatures Specific for Signaling Pathways 231
2.5 Prediction Model for Early HCC 233
3 Toward an Integrative Systems Genomics 234
3.1 Chromosomal Alterations and Epigenetic Abnormalities in HCC 234
3.2 Integrative Systems Genomics to Identify Potential Driver Genes in HCC 235
3.3 Toward a Personalized Medicine 236
References 237
13 Molecular Signatures of Hepatocellular Carcinoma Metastasis 240
1 Metastasis and the HCC Patient 240
2 Metastasis Models 241
2.1 Historical Metastasis Models 241
2.2 Contemporary Metastasis Models 244
2.2.1 The Dual Proclivity Metastasis Model 244
2.2.2 The Epigenetic Metastasis Model 245
2.2.3 The Microenvironment Metastasis Model 246
2.2.4 The Genetic Predisposition Metastasis Model 248
2.2.5 The Stem Cell/Epithelial--Mesencyhmal Transition (EMT) Metastasis Model 249
3 Metastasis and Clinical Treatment 249
4 Summary 251
References 252
14 Gene Mutations and Transcriptomic Profiles Associated to Specific Subtypes of Hepatocellular Tumors 257
1 Introduction 257
1.1 Hepatocellular Carcinomas 257
1.2 Benign Primary Liver Tumors 258
1.2.1 Hepatocellular Adenomas (HCA) 258
2 Oncogene and Tumor Suppressor Gene Mutations Define Specific Subgroups Of Hepatocellular Tumors 260
2.1 TP53 is the Tumor Suppressor the Most Frequently Mutated in HCC 260
2.2 CTNNB1 Coding for ß-Catenin is Frequently Mutated in HCC and HCA 260
2.3 Biallelic Mutations Inactivating HNF1 Are Frequent in HCA 262
2.4 gp130 Is Frequently Activated by Small in-Frame Deletions In Inflammatory HCA 262
2.5 Other Genetic Alterations Identified in Specific HCC Subgroups of Tumors 263
3 Comprehensive Molecular Profiling are Related to Genetic Alterations and Specific Tumor Subtypes 263
3.1 Genetic and Chromosomal Classification of Benign and Malignant Hepatocellular Tumors 263
3.2 Transcriptomic Classification of Benign and Malignant Hepatocellular Tumors 264
3.3 Micro-RNA Profiling in Hepatocellular Tumors 266
4 Conclusion 267
References 267
Part VII Cancer Stem Cells 274
15 Cancer Stem Cells and Liver Cancer 275
1 Cancer Stem Cells (CSC) 276
2 Definition and Isolation of Putative Cancer Stem Cells 279
2.1 Antigenic Markers 279
2.2 Functional Approaches 280
2.3 Side Population Approach (Hoechst-33342-Dye Staining) 280
2.4 ALDEFLUOR-Approach (ALDH-Activity) 281
2.5 Sphere Formation 282
3 Cancer Stem Cells and Hepatocellular Carcinoma (HCC) 283
4 Cancer Stem Cells and Metastasis/Circulating CSC 288
5 Clinical Implications of CSC for the Liver Cancer 289
References 290
16 Heterogeneity of Liver Cancer Stem Cells 296
1 Introduction 296
2 Liver Development and Stem-Cell Marker Expression 297
2.1 Early Stages of Embryogenesis 297
2.2 Hepatic Specification 298
2.3 Hepatocytic Differentiation 298
2.4 Hepatocytes as Stem Cells 299
2.5 Biliary Differentiation 299
3 Heterogeneity of Stem-Cell Marker Expression in Hepatic Progenitor Cells 299
3.1 Putative Hepatic Stem/Progenitor Cell Markers 299
3.2 Heterogeneity of Hepatic Progenitor Cells 300
3.3 Factors Affecting the Heterogeneity of Putative Hepatic Stem/Progenitor Cells 301
4 Liver Cancer as a Disease of Deregulated Stem Cells 302
4.1 The CSC Concept 302
4.2 Hepatocellular Carcinoma as a Disease of Stem Cells 303
4.3 Putative Liver Cancer Stem-Cell Markers 303
4.3.1 SP Fraction 303
4.3.2 ABCG2 304
4.3.3 CD133 (Prominin 1) 304
4.3.4 CD90 (Thy-1) 305
4.3.5 OV6 305
4.3.6 EpCAM (Epithelial Cell Adhesion/Activating Molecule, CD326) 305
4.4 Heterogeneity of Liver Cancer Stem Cells 306
5 Conclusions 308
References 308
17 Cancer Stem Cells in Liver Carcinoma 313
1 Introduction 313
2 The Cancer Stem-Cell Concept 315
3 Hepatocytes Have Stem Cell Properties 317
4 Hepatic Progenitor Cells are Activated in the Majority of Chronic Liver Diseases and form a Target Cell Population for Carcinogenesis 318
5 Liver Cancer with Progenitor Cell Phenotypical Features: Maturation Arrest or Dedifferentiation? 320
6 Potential Liver Cancer Stem Cell Markers 323
7 Conclusions 324
References 324
Part VIII Liver Cancer Genetics in the Clinic 328
18 Molecular Signaling in Hepatocellular Carcinoma 329
1 Overview 329
2 P53 and Rb-Associated Signaling Pathways 330
3 MAPKs Signaling Pathway 332
4 Wnt/-Catenin Signaling Pathway 333
5 TGF- Signaling Pathway 334
6 IKK/NF-B Signaling Pathway 334
7 PI3-K/Akt Signaling Pathway 335
8 JAK/STAT Signaling Pathway 336
9 Hedgehog Signaling Pathway 337
10 Notch Signaling Pathway 337
11 Stem-Cell Related Signaling Pathways 338
12 Peroration 339
References 339
19 Molecular Events on Metastasis of Hepatocellular Carcinoma 341
1 A Synopsis of Studies on Metastasis of Hepatocellular Carcinoma at Authors Institute 341
2 Molecular Events During Establishment of Metastatic Human HCC Models 343
2.1 Molecular Events During Establishment of Metastatic Human HCC Models 343
2.2 Molecular Events During Establishment of Metastatic Human HCC Cell Lines 344
3 Molecules Related to HCC Metastasis 345
3.1 Genomic Approach 345
3.1.1 Chromosome 8p Deletion Was Found to Be One of the Most Important Chromosomal Aberrations that Associate with Metastasis of HCC 345
3.1.2 Using ''8p-Specific'' Microarrays, Two Novel Metastatic Suppressors Were Identified, and Proved to Suppress In Vitro Invasion and In Vivo Metastasis of HCC 346
3.2 Proteomics Approach 347
4 Molecules for Prediction of HCC Metastasis 348
4.1 Chromosome 8p Deletion Detected in HCC Tissues or Circulating DNA of HCC Patients Can Predict HCC Recurrence and Patient's Prognosis 348
4.2 Plasma Level of Osteopontin (OPN) Can Be a Predictor for Recurrence and Prognosis of HCC Patients 349
4.3 Through Proteomics Analysis, CK19 and CK 10 Are Identified as Predictors for HCC Metastasis 350
5 Molecular Signature of HCC Metastasis 351
5.1 Molecular Signature of HCC Metastasis Derived from Tumor Gene Expression Profiling 351
5.2 Molecular Signature of HCC Metastasis Derived from Gene Expression Profiling of Non-tumor Liver Tissues 352
6 Molecular Events in Microenvironment with Special Reference to Tumor Vasculature 352
6.1 Angiogenesis of HCC 353
6.2 Inflammation-Related Microenvironment 354
7 Molecular Changes During Intervention of HCC Metastasis 354
7.1 Molecular Changes Induced by Anti-angiogensis Therapies 354
7.2 Molecular Changes During Interferon-Alpha Treatment 355
7.3 EMT (Epithelial to Mesenchymal Transition) Associates with Molecular Changes During Intervention 355
8 Future Prospects 356
References 356
20 Molecular Pathogenesis of Hepatocellular Carcinoma 364
1 Multistep Hepatocarcinogenesis 364
2 Genetic Alterations in Hepatocarcinogenesis 366
2.1 Chromosomal Abnormalities 366
2.2 Somatic Mutational Analysis 369
3 Epigenetic Alterations in Hepatocarcinogenesis 370
4 MicroRNA and HCC 373
5 Signaling Pathways in HCC 374
5.1 Wnt/-Catenin Pathway 374
5.2 Ras-Signaling Pathway 377
5.3 PI3K/Akt/mTOR Pathway 377
5.4 DLC1/Rho/ROCK Pathway 378
6 Perspective 379
References 379
Subject 
388