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xiii | |
Preface |
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xvii | |
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Chapter 1 Noncoding ribonucleic acid for pancreatic cancer therapy |
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1 | (16) |
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1 | (1) |
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1.2 Experimental methods and tools for analyzing noncoding RNAs in pancreatic cancer patients |
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2 | (1) |
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1.3 Bioinformatics for analyzing noncoding RNAs in pancreatic cancer patients |
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3 | (1) |
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3 | (1) |
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1.5 Pancreatic cancer---specific microRNAs |
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4 | (1) |
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1.6 Pancreatic cancer---associated IncRNAs |
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4 | (2) |
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1.7 Pancreatic cancer---associated circular RNAs |
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6 | (1) |
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1.8 Diagnostic microRNA markers of PDAC |
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7 | (1) |
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1.9 Diagnostic IncRNA markers of PDAC |
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7 | (2) |
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1.10 Diagnostic circular RNA markers of PDAC |
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9 | (1) |
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1.11 Summary and conclusion |
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9 | (8) |
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9 | (1) |
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9 | (8) |
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Chapter 2 Applications of noncoding RNAs in brain cancer patients |
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17 | (48) |
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17 | (4) |
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2.1.1 Types of brain cancer |
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17 | (2) |
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2.1.2 Types of ncRNAs and mechanism of action |
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19 | (1) |
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20 | (1) |
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2.2 Data sets for noncoding RNAs analysis |
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21 | (3) |
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2.2.1 RNA-seq deposits and data sets |
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24 | (1) |
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2.3 Expression of noncoding RNAs in brain cancer patients |
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24 | (6) |
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2.3.1 Sample types used for analyzing noncoding RNAs in brain |
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24 | (1) |
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2.3.2 Models to study ncRNA expression |
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24 | (2) |
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2.3.3 NcRNA expression profiles in cancer stem cells and their consequences on tumor development |
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26 | (4) |
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2.4 Experimental methods and tools for analyzing noncoding RNAs in brain cancer patients |
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30 | (5) |
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2.4.1 Studying ncRNA interactions with targets by luciferase assays and ncRNA---protein interactions by immunoprecipitation |
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30 | (1) |
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2.4.2 Validations of RNA-seq results by qRT-PCR and fluorescence in situ hybridization methods |
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31 | (4) |
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2.5 Noncoding RNAs as predictive marker for brain cancer patients |
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35 | (5) |
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2.5.1 Diagnostic potential of noncoding RNAs in brain cancer patients |
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35 | (2) |
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2.5.2 Prognostic potential of noncoding RNAs in brain cancer patients |
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37 | (3) |
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2.6 Potential of noncoding RNAs in predicting chemoresistance and radioresistance in brain cancer patients |
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40 | (5) |
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2.7 Therapeutic potential and targeting of ncRNAs in brain cancer patients---challenges and perspectives |
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45 | (2) |
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2.8 Summary and conclusions |
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47 | (18) |
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49 | (16) |
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Chapter 3 Noncoding RNAs in patients with colorectal cancer |
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65 | (32) |
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65 | (1) |
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3.2 Experimental methods and tools for analyzing noncoding RNAs in colorectal cancer patients |
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66 | (1) |
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67 | (1) |
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3.4 Serial analysis of gene expression |
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68 | (1) |
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3.5 Cap analysis gene expression |
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68 | (1) |
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69 | (1) |
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3.7 Dataset and bioinformatics for analyzing noncoding RNAs in colorectal cancer patients |
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70 | (2) |
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3.8 Expression of noncoding RNAs in colorectal cancer patients |
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72 | (4) |
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3.9 Sample types used for analyzing noncoding RNAs |
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76 | (1) |
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3.10 Cell signaling pathways modulated by noncoding RNAs in colorectal cancer patients |
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77 | (5) |
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3.10.1 Wnt/β-catenin signaling pathway |
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77 | (2) |
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3.10.2 JAK (Janus Kinase)/STAT (Signal Transducer and Activator of Transcription) signaling pathway |
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79 | (1) |
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3.10.3 PI3K (Phosphoinositide 3-Kinase)/PTEN (Phosphatase and Tensin Homolog)/AKT (AK Mouse Plus Transforming or Thymoma)/mTOR (Mechanistic Target of Rapamycin) signaling pathway |
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79 | (1) |
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3.10.4 Ras/MAPK (Mitogen-activated protein kinase)-signaling pathway |
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80 | (1) |
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3.10.5 P53 signaling pathway |
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80 | (1) |
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3.10.6 Notch signaling pathway |
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81 | (1) |
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3.10.7 NF-κB (Nuclear Factor Kappa B) signaling pathway |
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81 | (1) |
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3.11 Several other mechanisms |
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82 | (1) |
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3.11.1 Caspase cleavage cascade |
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82 | (1) |
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3.11.2 Chemokine signaling |
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82 | (1) |
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3.11.3 Interleukin pathway |
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82 | (1) |
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3.12 Clinical applications of noncoding RNAs as biomarkers in patients with colorectal cancer |
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82 | (1) |
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3.12.1 Noncoding RNAs as predictive markers for colorectal cancer patients |
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82 | (1) |
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3.13 Diagnostic potential of noncoding RNAs in colorectal cancer patients |
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83 | (1) |
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3.14 Prognostic potential of noncoding RNAs in colorectal cancer patients |
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84 | (1) |
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3.15 Therapeutic potential of noncoding RNAs in colorectal cancer patients |
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85 | (1) |
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3.16 Potential of noncoding RNAs in predicting chemoresistance and radioresistance in colorectal cancer patients |
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85 | (1) |
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86 | (11) |
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87 | (10) |
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Chapter 4 Applications of noncoding ribonucleic acids in multiple myeloma patients |
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97 | (44) |
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97 | (2) |
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4.2 Samples and experimental methods for the analysis of noncoding RNAs in multiple myeloma patients |
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99 | (1) |
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4.3 Datasets analyzing noncoding RNAs in multiple myeloma patients |
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100 | (8) |
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4.3.1 Datasets profiling expression of short noncoding RNAs in multiple myeloma |
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100 | (7) |
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4.3.2 Datasets profiling expression of long noncoding RNAs in multiple myeloma |
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107 | (1) |
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4.4 Noncoding RNAs implicated in the etiology of multiple myeloma |
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108 | (11) |
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4.4.1 MicroRNAs implicated in the etiology of multiple myeloma |
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108 | (5) |
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4.4.2 Long noncoding RNAs implicated in multiple myeloma |
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113 | (5) |
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4.4.3 Other ncRNAs implicated in multiple myeloma |
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118 | (1) |
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4.4.4 Interactions between ncRNAs in multiple myeloma |
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119 | (1) |
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4.5 Cell signaling pathways modulated by noncoding RNAs in multiple myeloma |
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119 | (5) |
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4.5.1 IL6/JAK/STAT signaling and noncoding RNAs in multiple myeloma |
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120 | (1) |
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4.5.2 Noncoding RNAs and the p53 pathway in multiple myeloma |
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121 | (2) |
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4.5.3 The influence of noncoding RNAs on PI3K/AKT/mTOR, MAPK, and NFκB signaling in multiple myeloma |
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123 | (1) |
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4.6 Noncoding RNAs affecting interactions with the bone marrow niche |
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124 | (1) |
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4.7 Noncoding RNAs as diagnostic and prognostic biomarkers in multiple myeloma |
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125 | (5) |
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4.8 Therapeutic potential of noncoding RNAs in multiple myeloma patients |
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130 | (1) |
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4.9 Summary and conclusion |
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131 | (10) |
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132 | (1) |
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132 | (9) |
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Chapter 5 Clinical applications of noncoding RNAs in lung cancer patients |
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141 | (36) |
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141 | (1) |
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142 | (1) |
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5.2 Experimental methods and tools for analyzing ncRNAs in lung cancer patients |
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143 | (1) |
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5.3 Datasets and informatics for analyzing ncRNAs in lung cancer patients |
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143 | (1) |
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5.4 Expression of ncRNAs in lung cancer patients |
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144 | (4) |
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145 | (1) |
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146 | (1) |
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5.4.3 Trna-derived small RNA |
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146 | (1) |
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146 | (1) |
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5.4.5 Small nucleolar RNA |
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147 | (1) |
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5.4.6 PIWI-interacting RNA |
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147 | (1) |
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5.4.7 Natural antisense transcripts |
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147 | (1) |
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5.4.8 Transcribed ultraconserved region |
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148 | (1) |
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5.5 Sample types used for analyzing ncRNAs |
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148 | (5) |
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148 | (2) |
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5.5.2 Bronchoalveolar lavage fluid |
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150 | (1) |
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151 | (1) |
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152 | (1) |
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5.6 Cell signaling pathways modulated by ncRNAs in lung cancer patients |
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153 | (2) |
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5.7 NcRNAs as predictive markers for lung cancer patients |
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155 | (3) |
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5.8 Diagnostic potential of ncRNAs in lung cancer patients |
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158 | (1) |
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5.8.1 LncRNAs as diagnostic markers |
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158 | (1) |
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5.8.2 Mirnas as diagnostic markers |
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159 | (1) |
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5.9 Prognostic potential of ncRNAs in lung cancer patients |
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159 | (2) |
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5.9.1 LncRNAs as prognostic biomarkers |
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159 | (1) |
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5.9.2 Mirnas as prognostic biomarkers |
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160 | (1) |
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5.10 Therapeutic potential of ncRNAs in lung cancer patients |
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161 | (1) |
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5.10.1 Therapeutic potential of IncRNAs |
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161 | (1) |
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5.10.2 Therapeutic potential of miRNAs |
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161 | (1) |
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5.11 Potential of ncRNAs in predicting chemoresistance and radioresistance in lung cancer patients |
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162 | (3) |
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5.11.1 NcRNAs and their role in chemoresistance |
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162 | (2) |
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5.11.2 NcRNAs and their role in radioresistance |
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164 | (1) |
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5.12 Summary and conclusion |
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165 | (12) |
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166 | (1) |
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166 | (11) |
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Chapter 6 Noncoding RNAs in intraocular tumor patients |
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177 | (34) |
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Maria Jose Blanco-Teijeiro |
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177 | (1) |
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178 | (12) |
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178 | (1) |
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6.2.2 Long noncoding RNAs and circular RNAs in retinoblastoma |
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178 | (6) |
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6.2.3 MicroRNAs in retinoblastoma |
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184 | (5) |
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6.2.4 Therapeutic potential of noncoding RNAs in retinoblastoma |
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189 | (1) |
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190 | (1) |
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190 | (10) |
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190 | (1) |
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6.3.2 Long noncoding RNAs in uveal melanoma |
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191 | (3) |
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6.3.3 MicroRNAs in uveal melanoma |
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194 | (5) |
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199 | (1) |
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200 | (11) |
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201 | (10) |
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Chapter 7 Applications of noncoding RNAs in renal cancer patients |
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211 | (74) |
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211 | (2) |
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7.2 Datasets and informatics for analyzing noncoding RNAs in renal cancer patients |
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213 | (15) |
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7.2.1 Datasets and informatics for analyzing microRNAs in renal cancers |
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213 | (1) |
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7.2.2 Datasets and informatics for analyzing long noncoding RNAs in renal cancers |
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214 | (1) |
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7.2.3 Datasets and informatics for analyzing circular RNAs in renal cancers |
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214 | (14) |
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7.3 Expression of noncoding RNAs in renal cancer patients |
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228 | (12) |
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7.3.1 Expression of microRNAs in renal cancer patients |
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228 | (1) |
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7.3.2 Expression of long noncoding RNAs in renal cancer patients |
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228 | (5) |
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7.3.3 Expression of circular RNAs in renal cancer patients |
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233 | (7) |
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7.4 Cell signaling pathways modulated by noncoding RNAs in renal cancer patients |
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240 | (3) |
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7.4.1 Cell signaling pathways modulated by microRNAs in renal cancer patients |
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241 | (1) |
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7.4.2 Cell signaling pathways modulated by long noncoding RNAs in renal cancer patients |
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242 | (1) |
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7.4.3 Cell signaling pathways modulated by circular RNAs in renal cancer patients |
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243 | (1) |
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7.5 Diagnostic potential of noncoding RNAs in renal cancer patients |
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243 | (3) |
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7.5.1 Diagnostic potential of microRNAs in renal cancer patients |
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243 | (2) |
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7.5.2 Diagnostic potential of long noncoding RNAs in renal cancer patients |
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245 | (1) |
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7.5.3 Diagnostic potential of circular RNAs in renal cancer patients |
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245 | (1) |
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7.6 Prognostic potential of noncoding RNAs in renal cancer patients |
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246 | (8) |
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7.6.1 Prognostic potential of miRNAs in RCC |
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246 | (2) |
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7.6.2 Prognostic potential of long noncoding RNAs in RCC |
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248 | (4) |
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7.6.3 Prognostic potential of circular RNAs in RCC |
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252 | (2) |
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7.7 Therapeutic potential of noncoding RNAs in renal cancer patients |
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254 | (2) |
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7.7.1 Therapeutic potential of microRNAs in renal cancer patients |
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254 | (1) |
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7.7.2 Therapeutic potential of long noncoding RNAs in renal cancer patients |
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254 | (1) |
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7.7.3 Therapeutic potential of circular RNAs in renal cancer patients |
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255 | (1) |
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7.8 Potential of noncoding RNAs in predicting chemoresistance and radioresistance in renal cancer patients |
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256 | (2) |
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7.8.1 Potential of microRNAs in predicting chemoresistance/radioresistance in renal cancer patients |
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256 | (1) |
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7.8.2 Potential of long noncoding RNAs in predicting chemoresistance/radioresistance in renal cancer patients |
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257 | (1) |
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7.8.3 Potential of ciRNAs in predicting chemoresistance/radioresistance in renal cancer patients |
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257 | (1) |
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7.9 Summary and conclusion |
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258 | (27) |
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259 | (26) |
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Chapter 8 Clinical significance of long noncoding RNAs in breast cancer patients |
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285 | (12) |
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285 | (1) |
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286 | (1) |
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8.2 Potential of IncRNAs in the diagnosis of breast cancer |
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287 | (1) |
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8.3 Potential of IncRNAs in the prognosis of breast cancer |
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288 | (1) |
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8.4 Potential of IncRNAs in breast cancer therapy |
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289 | (1) |
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8.5 Potential of IncRNAs in predicting breast cancer patient's response to therapeutics |
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290 | (1) |
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8.6 Potential of IncRNAs in predicting chemoresistance and radioresistance in breast cancer patients |
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290 | (1) |
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8.7 Experimental methods and tools for analyzing noncoding RNAs in cancer patients |
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291 | (1) |
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8.8 Summary and conclusion |
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292 | (5) |
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292 | (1) |
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292 | (5) |
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Chapter 9 Noncoding ribonucleic acids in gastric cancer patients |
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297 | (18) |
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297 | (3) |
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298 | (1) |
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298 | (1) |
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299 | (1) |
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9.1.4 Long noncoding RNAs |
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299 | (1) |
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9.2 Experimental methods and tools for analyzing noncoding RNAs in gastric cancer patients |
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300 | (2) |
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9.3 Expression of noncoding RNAs in gastric cancer patients |
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302 | (1) |
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9.4 Sample types used for analyzing noncoding RNAs (tumor biopsies, liquid biopsies, etc.) |
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303 | (1) |
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9.5 Cell signaling pathways modulated by noncoding RNAs in gastric cancer patients |
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304 | (2) |
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9.6 Noncoding RNAs as prognostic and predictive marker for gastric cancer patients |
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306 | (1) |
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9.7 Diagnostic value of small noncoding RNAs in gastric cancer |
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307 | (1) |
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9.8 Potential of noncoding RNAs in predicting chemotherapy resistance and radiotherapy resistance in gastric cancer patients |
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308 | (1) |
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9.9 Summary and conclusion |
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309 | (6) |
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310 | (5) |
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Chapter 10 Noncoding RNAs in prostate cancer patients |
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315 | (28) |
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315 | (2) |
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10.2 Experimental methods and tools for analyzing ncRNAs in prostate cancer patients |
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317 | (2) |
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10.2.1 NcRNA profiling in prostate cancer |
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317 | (1) |
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317 | (1) |
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317 | (1) |
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10.2.4 Ncrna validation in prostate cancer |
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317 | (1) |
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10.2.5 Investigation of ncRNA interactions |
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318 | (1) |
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10.2.6 Secondary structures of ncRNAs |
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319 | (1) |
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10.3 Datasets and informatics for analyzing noncoding RNAs |
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319 | (2) |
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10.3.1 Homology-based methods |
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319 | (1) |
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10.3.2 De novo methods for ncRNA predictions |
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320 | (1) |
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10.3.3 Special miRNA, circularRNA, and IncRNA databases |
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321 | (1) |
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10.4 Sample types used for analyzing ncRNAs (tumor biopsies, liquid biopsies, etc.) |
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321 | (1) |
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10.4.1 New aspects of RNA-based biomarkers discovery in prostate cancer |
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322 | (1) |
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10.4.2 Prostate cancer biospecimen repositories |
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322 | (1) |
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10.5 Cell signaling pathways modulated by ncRNAs in prostate cancer |
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322 | (4) |
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10.5.1 Phosphatase and tensin homolog/phosphoinositide 3-kinase/AkT/mammalian target of rapamycin pathway |
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323 | (1) |
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10.5.2 Mitogen-activated protein kinase pathway |
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324 | (1) |
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325 | (1) |
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10.5.4 AR signaling pathway |
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325 | (1) |
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10.6 NcRNAs as biomarkers for prostate cancer |
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326 | (4) |
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327 | (1) |
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327 | (1) |
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328 | (2) |
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10.7 Therapeutic potential of ncRNAs in prostate cancer patients |
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330 | (1) |
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10.8 Potential of ncRNAs in predicting chemo-resistance and radioresistance in prostate cancer patients |
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331 | (1) |
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331 | (1) |
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332 | (1) |
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332 | (11) |
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333 | (10) |
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Chapter 11 Noncoding RNAs in liver cancer patients |
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343 | (48) |
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343 | (2) |
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345 | (3) |
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345 | (1) |
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346 | (2) |
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11.2 NcRNA roles in liver development and functions |
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348 | (3) |
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348 | (2) |
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11.2.2 Long noncoding RNAs |
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350 | (1) |
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11.3 Noncoding RNA detection |
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351 | (4) |
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11.3.1 Tissular versus circulating ncRNAs |
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351 | (1) |
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11.3.2 Methods of ncRNA analyses |
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352 | (3) |
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11.4 Expression of ncRNAs in liver cancers |
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355 | (5) |
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355 | (3) |
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11.4.2 Long noncoding RNAs |
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358 | (2) |
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11.5 Noncoding RNA relevance in liver cancer diagnosis and prognosis |
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360 | (9) |
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11.5.1 Noncoding RNA as potential diagnostic tools |
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360 | (3) |
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11.5.2 Prognostic potential of noncoding RNAs in liver cancer patients |
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363 | (1) |
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11.5.3 Noncoding RNAs as predictive markers for liver cancer patients |
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364 | (1) |
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11.5.4 Roles of microRNA in drug resistance |
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365 | (1) |
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11.5.5 Therapeutic potential of noncoding RNAs in liver cancer patients |
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366 | (3) |
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11.6 Summary and conclusion |
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369 | (22) |
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370 | (1) |
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370 | (21) |
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Chapter 12 Noncoding ribonucleic acids in gallbladder cancer patients |
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391 | (18) |
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391 | (2) |
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12.2 MiRNAs in gallbladder carcinoma |
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393 | (4) |
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12.2.1 Biogenesis and biological functions of miRNA |
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393 | (1) |
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12.2.2 MicroRNAs in pathogenesis and as a therapeutic target in gallbladder carcinoma |
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393 | (3) |
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12.2.3 MicroRNAs as biomarkers in gallbladder carcinoma |
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396 | (1) |
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12.3 LncRNAs in gallbladder carcinoma |
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397 | (5) |
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12.3.1 Biogenesis and biological functions of LncRNA |
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398 | (1) |
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12.3.2 LncRNAs in pathogenesis and as a therapeutic target in gallbladder carcinoma |
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398 | (3) |
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12.3.3 LncRNA as a biomarker |
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401 | (1) |
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12.4 PiRNAs in gallbladder carcinoma |
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402 | (1) |
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12.5 Limitations of clinical utility of ncRNAs in gallbladder carcinoma |
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403 | (1) |
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403 | (6) |
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404 | (5) |
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Chapter 13 Clinical implications of noncoding ribonucleic acids in neuroblastoma patients |
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409 | (24) |
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409 | (1) |
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13.2 Types of noncoding RNAs |
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410 | (2) |
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410 | (1) |
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13.2.2 Long noncoding RNAs |
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410 | (1) |
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13.2.3 P-element-induced wimpy testis (Piwi)-interacting RNAs |
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411 | (1) |
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411 | (1) |
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13.3 Role of noncoding RNAs in neuroblastoma growth and development |
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412 | (4) |
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412 | (1) |
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13.3.2 Long noncoding RNAs |
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413 | (2) |
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13.3.3 P-element-induced wimpy testis (Piwi)-interacting RNAs |
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415 | (1) |
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415 | (1) |
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13.4 Clinical significance of noncoding RNAs in neuroblastoma |
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416 | (3) |
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|
416 | (1) |
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13.4.2 Long noncoding RNAs |
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|
417 | (1) |
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13.4.3 P-element-induced wimpy testis (Piwi)-interacting RNAs |
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418 | (1) |
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|
419 | (1) |
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13.5 Therapeutic implications and targeting strategies for noncoding RNAs in neuroblastoma |
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|
419 | (3) |
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13.5.1 Therapeutic potential of noncoding RNAs in neuroblastoma |
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|
419 | (1) |
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13.5.2 Targeting strategies for noncoding RNAs |
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|
420 | (2) |
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|
422 | (11) |
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|
423 | (1) |
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|
423 | (1) |
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|
424 | (9) |
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Chapter 14 Potential clinical application of IncRNAs in pediatric cancer |
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|
433 | (16) |
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|
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|
|
433 | (2) |
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|
433 | (1) |
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14.1.2 Long noncoding RNA |
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|
434 | (1) |
|
14.2 Experimental and bioinformatics tools for studying IncRNAs |
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|
435 | (2) |
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14.3 LncRNAs in pediatric cancer |
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|
437 | (7) |
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|
437 | (4) |
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|
441 | (1) |
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|
442 | (1) |
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|
443 | (1) |
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|
443 | (1) |
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14.4 Conclusion and perspectives |
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|
444 | (5) |
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|
444 | (1) |
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|
445 | (4) |
Index |
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449 | |