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xix | |
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1 | (26) |
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1 | (1) |
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2 | (9) |
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Tumor, Node, Metastasis Staging of Cancer |
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11 | (2) |
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Molecular Delineation of Cancer |
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13 | (5) |
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Genetic Alteration Signatures in Cancer |
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13 | (2) |
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Competing Endogenous RNAs Hypothesis |
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15 | (2) |
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Epigenetic Alteration Signatures in Cancer |
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17 | (1) |
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Therapeutic Potential of Noncoding RNA in Cancer |
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18 | (1) |
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18 | (9) |
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SECTION 1 NON-CODING RNAs: FINE-TUNING CANCER |
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Chapter 2 miRNA and Cancer: A Deadly Liaison? |
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27 | (20) |
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27 | (3) |
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Cell Cycle, Proliferation, and Survival |
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30 | (1) |
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Angiogenesis and Metastasis |
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31 | (2) |
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33 | (5) |
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Cancer Stem Cells and Chemoresistance |
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38 | (3) |
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41 | (1) |
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41 | (1) |
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41 | (6) |
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Chapter 3 Alteration of MicroRNA Biogenesis Pathways in Cancers |
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47 | (12) |
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47 | (1) |
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MicroRNA Biogenesis Pathway in Animals |
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48 | (1) |
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Alteration in MicroRNA Transcription |
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49 | (1) |
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Alteration in Primary MicroRNA Processing in Nucleus |
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50 | (2) |
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Alteration in Pre-MicroRNA Export Into Cytoplasm |
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52 | (1) |
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Alteration in Cytoplasmic Pre-MicroRNA Processing |
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52 | (1) |
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Alteration in RNA-Induced Silencing Complex |
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52 | (1) |
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53 | (1) |
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54 | (5) |
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Chapter 4 MicroRNAs in Exosomes in Cancer |
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59 | (20) |
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59 | (1) |
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Introduction to MicroRNAs |
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60 | (1) |
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Brief Description of Canonical MicroRNA Biogenesis |
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60 | (2) |
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Brief Description of MicroRNA Function |
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62 | (1) |
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Brief Description of Exosomes |
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62 | (1) |
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Brief Description of Exosomal Sorting of MicroRNAs |
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63 | (1) |
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Exosomal MicroRNA in Cancer---Invasion and Metastasis |
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64 | (1) |
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Exosomal MicroRNA in Cancer---Angiogenesis |
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65 | (1) |
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Exosomal MicroRNAs in Cancer---Regulating Metabolism |
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66 | (1) |
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Exosomal MicroRNA in Cancer---Cross Talk With the Immune System |
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67 | (2) |
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Exosomal MicroRNA in Cancer---Chemoresistance and Chemosensitivity |
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69 | (1) |
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Exosomal MicroRNA in Cancer---Potential Biomarkers and Liquid Biopsy |
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70 | (1) |
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Exosomal MicroRNA in Cancer---Conclusion |
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71 | (1) |
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List of Acronyms and Abbreviations |
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71 | (1) |
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72 | (1) |
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72 | (7) |
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Chapter 5 Circulating miRNAs Increasing the Risk of Cancer |
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79 | (16) |
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79 | (1) |
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How Circulating miRNAs Are Found in Blood Samples |
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80 | (2) |
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Discovery of Circulating miRNA |
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80 | (1) |
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80 | (2) |
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Why Circulating miRNAs Are Becoming an Increasing Risk |
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82 | (2) |
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Circulating miRNA is Able to Shuttle Between Different Cells |
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82 | (1) |
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Secreted miRNAs Can Serve as Signaling Molecules Mediating Intercellular Communication |
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82 | (2) |
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Circulating miRNAs Can Be Used as an Early Detection Technique |
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84 | (4) |
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The Diagnostic Potential of miRNAs in Various Cancers |
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84 | (2) |
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Challenges in Utilizing miRNAs as Circulating Biomarkers |
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86 | (2) |
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The Therapeutic Implications of miRNAs |
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88 | (1) |
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Conclusion and Future Perspectives |
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89 | (1) |
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90 | (5) |
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Chapter 6 Long Noncoding RNAs as Cancer Biomarkers |
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95 | (20) |
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Introduction: "Junk DNA," the New Key Player in Development and Disease |
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96 | (1) |
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Long Noncoding RNAs as Cancer Biomarkers |
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97 | (9) |
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97 | (3) |
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Potential Usage as Diagnostic and Prognostic Biomarkers of Different Tumors |
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100 | (6) |
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Conclusions and Future Perspectives |
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106 | (1) |
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List of Acronyms and Abbreviations |
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107 | (1) |
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108 | (1) |
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109 | (1) |
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109 | (6) |
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Chapter 7 The Balancing Act: Understanding MicroRNA and Competing Endogenous RNA Regulation in Cancer |
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115 | (16) |
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115 | (1) |
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Established Players in Competing Endogenous RNA Networks |
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116 | (4) |
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MicroRNAs---Key Linchpins in Competing Endogenous RNA Networks |
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116 | (1) |
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117 | (1) |
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118 | (1) |
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119 | (1) |
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Potential New Players in Competing Endogenous RNA Regulation |
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120 | (2) |
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120 | (1) |
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121 | (1) |
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122 | (3) |
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125 | (1) |
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125 | (1) |
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125 | (6) |
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Chapter 8 PIWI-Interacting RNAs (piRNAs) and Cancer |
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131 | (20) |
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Introduction: Small Noncoding RNAs |
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132 | (1) |
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Origins of PIWI-Interacting RNAs |
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132 | (4) |
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PIWI-Interacting RNA Clusters |
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132 | (1) |
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PIWI-Interacting RNA Pathway Genes |
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133 | (3) |
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The PIWI-Interacting RNA Pathway |
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136 | (1) |
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PIWI-Interacting RNA Biogenesis |
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136 | (1) |
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Functions of PIWI-Interacting RNAs |
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137 | (2) |
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Transposable Elements Are Parasites of the Genome |
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137 | (1) |
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PIWI-Interacting RNAs Function in Silencing Transposable Elements |
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138 | (1) |
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Potential Roles Beyond Transposable Elements |
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138 | (1) |
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Emerging Roles of the PIWI-Interacting RNA Pathway in Cancer |
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139 | (4) |
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Emerging Importance of the PIWI-Interacting RNA Pathway in Cancer |
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139 | (1) |
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PIWI-Interacting RNAs in Cancer |
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139 | (2) |
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141 | (2) |
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Future Directions and Conclusion |
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143 | (1) |
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List of Acronyms and Abbreviations |
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144 | (1) |
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145 | (6) |
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Chapter 9 Transfer RNA in Cancer |
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151 | (12) |
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151 | (1) |
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tRNA Mediates Translation of Proliferating Cancer Cells |
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152 | (1) |
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tRNA Functions Beyond Translation in Cancer |
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153 | (2) |
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Role of tRNA-Derived Fragments in Cancer Predisposition |
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155 | (3) |
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tRNA Acts as an Anticancer Drug Target and Therapeutic Agent |
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158 | (1) |
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159 | (1) |
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159 | (4) |
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Chapter 10 Dynamic Regulation of tRNA Modifications in Cancer |
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163 | (24) |
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163 | (1) |
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Transfer RNA Modifications |
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164 | (2) |
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Transfer RNA Modifications and Their Detection |
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166 | (1) |
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Transfer RNA Modifications and Cancer---An Overview |
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167 | (1) |
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Transfer RNA Modification Genes in Cancer |
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167 | (7) |
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168 | (2) |
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Cytosine Transfer RNA Methyltransferases |
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170 | (1) |
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Modifications at Wobble Uridine 34 (U34) |
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171 | (3) |
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174 | (1) |
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Dynamics of Transfer RNA Modifications in Cancer |
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174 | (3) |
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177 | (1) |
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177 | (10) |
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Chapter 11 Circular RNA: A Novel Noncoding RNA in Cancer |
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187 | (16) |
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187 | (1) |
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The Discovery of Circular RNA |
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188 | (2) |
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The Biogenesis of Circular RNA |
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190 | (1) |
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The Properties of Circular RNA |
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191 | (3) |
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The Identification of Circular RNA |
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194 | (1) |
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The Profile of Circular RNA in Cancer |
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195 | (1) |
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The Function of Circular RNA in Cancer |
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196 | (1) |
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The Mechanisms of Circular RNA in Cancer |
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196 | (2) |
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197 | (1) |
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197 | (1) |
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Transcription or Splicing Regulation |
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197 | (1) |
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198 | (1) |
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The Clinical Implication of Circular RNA in Cancer |
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198 | (1) |
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198 | (1) |
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199 | (1) |
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199 | (1) |
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List of Acronyms and Abbreviations |
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199 | (1) |
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200 | (3) |
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Chapter 12 Antisense RNA and Cancer |
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203 | (26) |
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205 | (1) |
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Antisense RNA: Definition and Classification |
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205 | (2) |
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205 | (1) |
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Naturally Occurring Antisense RNA |
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206 | (1) |
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206 | (1) |
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Natural Antisense Transcripts |
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207 | (1) |
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Non-Protein-Coding Natural Antisense Transcripts |
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207 | (1) |
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Protein-Coding Natural Antisense Transcripts: mRNAs as Natural Antisense Transcripts |
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207 | (1) |
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Antisense Long Noncoding RNA: Long Noncoding RNA Antisense to mRNA |
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208 | (1) |
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Long Noncoding Antisense RNA: The Antisense Transcript of Long Noncoding RNA |
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208 | (1) |
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209 | (1) |
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Endogenous Small Interference RNA |
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209 | (1) |
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209 | (1) |
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210 | (1) |
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210 | (1) |
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210 | (1) |
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210 | (1) |
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211 | (1) |
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Nonnatural Artificial as Antisense RNA |
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211 | (1) |
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211 | (1) |
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Anti-miRNA Antisense Inhibitor or Anti-miRNA Antisense Oligonucleotide |
|
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211 | (1) |
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Antisense RNA: The Mode of Action With Multiple Mechanisms |
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212 | (1) |
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RNA Cleavage Through RNA Interference |
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212 | (1) |
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212 | (1) |
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213 | (1) |
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Transcriptional Interference and Attenuation |
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213 | (1) |
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213 | (1) |
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213 | (1) |
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Antisense RNA and Carcinogenesis |
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214 | (1) |
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Aberrant Expression of Antisense RNAs in Cancers |
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214 | (2) |
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216 | (2) |
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Tumor Suppressor Antisense RNAs |
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218 | (1) |
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Antisense RNA Technologies: Potential Applications to Cancer Therapy |
|
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219 | (1) |
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219 | (1) |
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RNA Interference Technology |
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219 | (1) |
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MicroRNA Interference Technology |
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220 | (1) |
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220 | (1) |
|
List of Acronyms and Abbreviations |
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221 | (1) |
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222 | (1) |
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223 | (6) |
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Chapter 13 Implication of Other Noncoding RNAs in Cancer |
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229 | (18) |
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229 | (1) |
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230 | (4) |
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230 | (1) |
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Biogenesis and Function of Small Nucleolar RNAs |
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230 | (2) |
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The Role of Small Nucleolar RNAs in Cancer |
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232 | (2) |
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Telomeric Repeat-Containing RNA |
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234 | (2) |
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234 | (1) |
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Biogenesis and Functional Regulation of Telomeric Repeat-Containing RNA |
|
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234 | (2) |
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Telomeric Repeat-Containing RNA and Cancer |
|
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236 | (1) |
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Transfer RNA-Derived Small RNA |
|
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236 | (2) |
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Biogenesis and Function of Transfer RNA-Derived Small RNA |
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236 | (2) |
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Transfer RNA--Derived Small RNA and Cancer |
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238 | (1) |
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238 | (1) |
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239 | (1) |
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239 | (1) |
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240 | (7) |
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SECTION 2 GENETIC DYSREGULATION OF NON-CODING RNA IN CANCER |
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Chapter 14 Noncoding RNA Alterations in Cancer Molecular Pathways |
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247 | (22) |
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247 | (2) |
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Nuclear Factor-κB Signaling Pathway |
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249 | (3) |
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Receptor Tyrosine Kinase Signaling Pathway |
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252 | (1) |
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Mitogen-Activated Protein Kinase/ERK Pathway |
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253 | (2) |
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Phosphatidylinositol-3-Kinase/Protein Kinase B Signaling Pathway |
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255 | (2) |
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Transforming Growth Factor-β Signaling Pathway |
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257 | (1) |
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258 | (2) |
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260 | (1) |
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Hedgehog Signaling Pathway |
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261 | (1) |
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262 | (1) |
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262 | (6) |
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268 | (1) |
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Chapter 15 Genetic Alteration of MicroRNA Affecting Cancer Pathways |
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269 | (20) |
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270 | (1) |
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Biological Evidence of MicroRNA Mutations and Diseases Associations |
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271 | (2) |
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Single-Nucleotide Polymorphism Affecting MicroRNA Transcription |
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273 | (1) |
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Single-Nucleotide Polymorphism Affecting MicroRNA Maturation |
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273 | (2) |
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Single Nucleotide Polymorphism Affecting MicroRNA Targeting |
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275 | (1) |
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Computational Resources to Study Phenotypes at System Level |
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276 | (1) |
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Computational Resources to Study the Single-Nucleotide Polymorphisms Effects on Cancer |
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277 | (5) |
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282 | (1) |
|
List of Acronyms and Abbreviations |
|
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282 | (1) |
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282 | (1) |
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283 | (6) |
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Chapter 16 Genetic Variations of Long Noncoding RNAs in Cancer |
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289 | (22) |
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290 | (1) |
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Challenges to the Comprehensive Characterization of the Noncoding Mutational Landscape in Human Cancer |
|
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291 | (1) |
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Many Germline Cancer-Associated Single-Nucleotide Polymorphisms are Located in Long Noncoding RNA Loci |
|
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291 | (1) |
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Functional Characterization of Long Noncoding RNA-Associated Single-Nucleotide Polymorphisms |
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292 | (6) |
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Somatic Variations of Long Noncoding RNAs in Human Cancer |
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298 | (1) |
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Focal Amplification of Long Noncoding RNAs |
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299 | (2) |
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301 | (1) |
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List of Acronyms and Abbreviations |
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302 | (1) |
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303 | (8) |
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SECTION 3 EPIGENETIC EFFECT ON CANCER THROUGH NON-CODING RNAs |
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Chapter 17 Cross Talk Between Noncoding RNAs and DNA Methylation and Demethylation in Cancer |
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311 | (18) |
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311 | (1) |
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Overview of Noncoding RNAs in Cancer |
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312 | (2) |
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312 | (1) |
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Long Noncoding RNAs in Cancer |
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313 | (1) |
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Other Noncoding RNAs in Cancer |
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314 | (1) |
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DNA Methylation and Demethylation of Noncoding RNAs in Cancer |
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314 | (4) |
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DNA Methylation of MicroRNAs in Cancer |
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315 | (1) |
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DNA Methylation of Long Noncoding RNAs in Cancer |
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316 | (2) |
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DNA Methylation of Other Noncoding RNAs in Cancer |
|
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318 | (1) |
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Noncoding RNAs--Mediated DNA Methylation and Demethylation in Cancer |
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318 | (2) |
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MicroRNA-Mediated DNA Methylation and Demethylation |
|
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318 | (1) |
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Long Noncoding RNA-Mediated DNA Methylation and Demethylation |
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319 | (1) |
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320 | (1) |
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320 | (1) |
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321 | (1) |
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321 | (8) |
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Chapter 18 Noncoding RNAs Act as a Chromatin Scaffold of Histone Modification Complexes in Cancer |
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329 | (30) |
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330 | (1) |
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Long Noncoding RNAs in Cancer |
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331 | (3) |
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Long Noncoding RNAs in Tumor Maintenance |
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332 | (1) |
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Long Noncoding RNAs in Tumor Progression |
|
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332 | (2) |
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Methods to Study Long Noncoding RNA |
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334 | (3) |
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Determination of Cellular Localization |
|
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336 | (1) |
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Study of Long Noncoding RNA-Protein Interaction |
|
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336 | (1) |
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Study of Long Noncoding RNA-DNA Interaction |
|
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336 | (1) |
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Study of Long Noncoding RNA-RNA Interaction |
|
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336 | (1) |
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Mechanism of Long Noncoding RNA Recruitment and Regulation of Their Target Genes |
|
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337 | (2) |
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Long Noncoding RNA Action in Cis |
|
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337 | (2) |
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Long Noncoding RNA Action in Trans |
|
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339 | (1) |
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Long Noncoding RNAs Function as Chromatin Scaffold |
|
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339 | (5) |
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Long Noncoding RNAs in DNA Methylation |
|
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340 | (1) |
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Long Noncoding RNAs in Chromatin Looping and Nucleosome Positioning |
|
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340 | (1) |
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Long Noncoding RNAs in Histone Modification |
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341 | (3) |
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Other Functions of Long Noncoding RNAs |
|
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344 | (2) |
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Long Noncoding RNAs Function as Natural Antisense Transcripts |
|
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344 | (1) |
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Long Noncoding RNAs as Competing Endogenous RNAs or Sponge RNAs |
|
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345 | (1) |
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Long Noncoding RNAs Function as Enhancer RNAs |
|
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345 | (1) |
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346 | (1) |
|
List of Acronyms and Abbreviations |
|
|
346 | (3) |
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349 | (3) |
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352 | (1) |
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352 | (7) |
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Chapter 19 Heterochromatin Modulation and PcG Control of Gene Expression Mediated by Noncoding RNA in Cancer |
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359 | (14) |
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359 | (1) |
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360 | (1) |
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Epigenetic Regulation of Transcription, Polycomb Repressive Complexes 1 and 2, and Heterochromatin |
|
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360 | (3) |
|
Polycomb Repressive Complexes and Long Noncoding RNAs |
|
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363 | (1) |
|
Long Noncoding RNAs in Tumor Angiogenesis |
|
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364 | (2) |
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366 | (1) |
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366 | (7) |
|
Chapter 20 Epigenetic Control of MicroRNA Expression and Cancer |
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373 | (8) |
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Epigenetic Control of MicroRNAs in Cancer |
|
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373 | (2) |
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Chromatic Modifying Machinery as a Target of MicroRNAs in Cancer |
|
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375 | (2) |
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Epigenetic Anticancer Therapies and MicroRNA Expression |
|
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377 | (1) |
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378 | (3) |
|
Chapter 21 Implications of Long Noncoding RNAs in Cancer Epigenetics |
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381 | (28) |
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381 | (2) |
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Characteristics of Long Noncoding RNAs |
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383 | (3) |
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Long Noncoding RNA Transcription and Stability |
|
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383 | (1) |
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Long Noncoding RNA Secondary Structures and Long Noncoding RNA-Protein Interactions |
|
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384 | (1) |
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Cell-Type Specificity of Long Noncoding RNAs |
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385 | (1) |
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Long Noncoding RNA-Mediated Mechanisms That are Linked to Cancer Epigenetics |
|
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386 | (1) |
|
Long Noncoding RNA-Mediated Imprinting and Chromatin Silencing |
|
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386 | (7) |
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Long Noncoding RNA-Mediated Regulation of Long Range Chromatin Silencing and Activation |
|
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387 | (2) |
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Long Noncoding RNAs Associated With Genome Stability and DNA Repair |
|
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389 | (1) |
|
Long Noncoding RNAs Associated With Nuclear Bodies |
|
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390 | (1) |
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391 | (2) |
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393 | (1) |
|
List of Acronyms and Abbreviations |
|
|
393 | (1) |
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394 | (1) |
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395 | (1) |
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|
395 | (14) |
|
SECTION 4 THERAPEUTIC IMPLICATIONS OF NON-CODING RNA IN CANCER |
|
|
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Chapter 22 Long Noncoding RNAs: Insight Into Their Roles in Normal and Cancer Stem Cells |
|
|
409 | (20) |
|
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410 | (1) |
|
Role of Long Noncoding RNAs in Normal Tissue Homeostasis |
|
|
410 | (6) |
|
Evidence for Involvement in Self-Renewal and Tissue Regeneration |
|
|
410 | (1) |
|
Mechanistic Role in Regulation |
|
|
411 | (5) |
|
Association of Long Noncoding RNAs with the Transformed Cellular Phenotype Through Generation and Regulation of Cancer Stem Cells |
|
|
416 | (6) |
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|
416 | (4) |
|
Long Noncoding RNAs as Regulators of Cancer Stem Cells in Other Cancers |
|
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420 | (2) |
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422 | (1) |
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422 | (1) |
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423 | (6) |
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Chapter 23 Clinical Relevance, Prognostic Potential, and Therapeutic Strategies of Noncoding RNAs in Cancer |
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429 | (18) |
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429 | (3) |
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The Role of Noncoding RNAs in Gene Expression |
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429 | (2) |
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Noncoding RNA Nomenclature |
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431 | (1) |
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A Brief History of Noncoding RNAs |
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431 | (1) |
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Noncoding RNA Biology and Mechanism of Action |
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432 | (2) |
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Is There Any Role for Noncoding RNAs in Cancer Diagnosis? |
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434 | (1) |
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Noncoding RNAs: Added Value in Staging? |
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435 | (1) |
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Noncoding RNA-Directed Therapy in Cancer: The Next Frontier in Anticancer Treatment? |
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436 | (4) |
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440 | (1) |
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440 | (1) |
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441 | (6) |
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Chapter 24 Noncoding RNAs: Novel Targets in Anticancer Drug Development |
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447 | (16) |
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448 | (1) |
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Clinical Relevance of Noncoding RNAs |
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448 | (7) |
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449 | (2) |
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451 | (2) |
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453 | (1) |
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454 | (1) |
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454 | (1) |
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455 | (1) |
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456 | (1) |
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456 | (1) |
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456 | (1) |
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457 | (1) |
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457 | (6) |
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SECTION 5 BIOINFORMATICS' DETECTION OF NON-CODING RNA IN CANCER |
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Chapter 25 Cancer Noncoding RNA Discovery Through High-Throughput Sequencing |
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463 | (16) |
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463 | (2) |
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Analyses of RNA-Seq Data From Clinical Samples |
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465 | (1) |
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Databases for RNA-Seq Data |
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465 | (2) |
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Discovery of Noncoding RNAs Using Sequencing Technologies |
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467 | (1) |
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Computational Infrastructure |
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468 | (2) |
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Using Bioinformatics for the Discovery of Noncoding RNAs in Cancer Models |
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470 | (3) |
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473 | (1) |
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473 | (3) |
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476 | (3) |
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Chapter 26 Noncoding RNAs as a Cause of Cancer: Evidence From Genome-Wide Association Studies and Reverse Genetics |
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479 | (18) |
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479 | (2) |
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Genome-Wide Association Studies on Noncoding RNAs and Cancer |
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481 | (5) |
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Principle Approaches or Genome-Wide Association Studies |
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481 | (1) |
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Cancer-Associated Noncoding RNA-Single-Nucleotide Polymorphisms |
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482 | (4) |
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MicroRNA Binding Site Polymorphisms as Potential Biomarkers of Cancer Risk |
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486 | (1) |
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Noncoding RNAs as Diagnostic Markers, Oncogenes, and Tumor Suppressors in Cancer |
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486 | (2) |
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Role of Noncoding RNAs in Cancers |
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488 | (1) |
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Noncoding RNAs as Cancer Therapeutic Targets and Agents |
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489 | (1) |
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490 | (1) |
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491 | (1) |
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491 | (6) |
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Chapter 27 A Comparative Evaluation of Emerging Databases and Tools for Cancer Noncoding RNAs |
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497 | (12) |
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498 | (7) |
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498 | (3) |
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501 | (1) |
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501 | (1) |
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501 | (1) |
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502 | (1) |
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502 | (1) |
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502 | (1) |
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502 | (1) |
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502 | (1) |
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502 | (1) |
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502 | (1) |
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503 | (1) |
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Pancreatic Cancer Database |
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503 | (1) |
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503 | (1) |
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503 | (1) |
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503 | (1) |
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503 | (1) |
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503 | (1) |
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504 | (1) |
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504 | (1) |
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504 | (1) |
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504 | (1) |
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The Cancer LncRNome Atlas |
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504 | (1) |
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504 | (1) |
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504 | (1) |
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Major Tools for Noncoding RNA Detection and Analyses |
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505 | (1) |
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505 | (1) |
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505 | (1) |
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Details About Our Database |
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505 | (1) |
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506 | (1) |
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506 | (3) |
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Chapter 28 Future Directions and Challenges Involved in Cancer Noncoding RNomics |
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509 | (16) |
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509 | (1) |
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Prediction of miRNA Genes From Small RNA Sequencing Data |
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510 | (2) |
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High-Throughput Long Noncoding RNA Profiling: Future Directions and Challenges |
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512 | (1) |
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Identification of Circulating Noncoding RNAs in Cancer: Challenges and Future Perspectives |
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513 | (3) |
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514 | (1) |
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514 | (1) |
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515 | (1) |
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Normalization and Data Analysis |
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515 | (1) |
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Challenges of Single Cell RNA Sequencing |
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516 | (2) |
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Challenges in Single Cell Isolation |
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517 | (1) |
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Challenges of Single Cell RNA Sequencing Library Preparation |
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517 | (1) |
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518 | (1) |
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List of Acronyms and Abbreviations |
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519 | (1) |
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519 | (6) |
Index |
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525 | |