Therapeutic Ribonucleic Acids in Brain Tumors (eBook)

Therapeutic Ribonucleic Acids in Brain Tumors 2
Preface 5
Contents 9
Contributors 11
Molecular Biology of Malignant Gliomas 17
1 Introduction 18
2 Altered Pathways Involved in Human Gliomas 19
2.1 pRb/E2F Axis in Human Gliomas 19
2.2 P53/MDM2/p14-ARF 20
2.3 PI3K/PTEN/Akt/PKB 25
2.4 EGFR 25
2.5 PDGF and PDGFR 27
2.6 VEGFR 27
2.7 K-Ras/Raf/MAPK 27
3 Lessons from Microarray Studies 28
4 Glioma Stem-Like Cells 33
5 Challenges for Therapies 35
References 35
Molecular Neurooncology and Neoangiogenesis of Malignant Gliomas 39
1 Molecular Pathways in Malignant Gliomas 41
1.1 Genetic Pathways of Primary (De Novo) and Secondary Glioblastomas 42
1.2 Major Signaling Pathways Regulating Tumor Growth 46
1.2.1 EGF/EGFR Signaling Pathway 46
1.2.2 PDGF/PDGFR Signaling Pathway 48
1.2.3 TGF/TGF-R Signaling Pathway 48
1.2.4 FGF/FGFR Signaling Pathway 50
1.2.5 IGF/IGFR Signaling Pathway 50
1.2.6 Gas6/Axl Signaling Pathway 50
1.3 Major Signaling Pathways Regulating Tumor-Angiogenesis 51
1.3.1 VEGF/VEGFR Signaling Pathway 51
1.3.2 Angiopoietins 53
1.3.3 Integrins 53
1.4 Major Intracellular Signal Transduction Pathways 54
1.4.1 Ras Signal Transduction 54
1.4.2 PI3K/Akt/PTEN/mTOR Signaling Pathway 54
2 Neoangiogenesis in Malignant Gliomas 55
2.1 Cellular Mechanisms 56
2.2 Molecular Mechanisms 56
2.3 Structural Abnormalities of Brain Tumor Blood Vessels and Blood Brain Barrier 58
2.4 Tumor Edema in Malignant Gliomas 60
Attendum 60
Growth Factor Receptors 60
Ras-GDP Pathway 60
PI3K Pathway 61
References 62
Molecular Therapies for Malignant Gliomas 72
1 Principles of Molecular Targeted Therapies 74
1.1 Monoclonal Antibodies 74
1.2 Small Molecule Inhibitors 75
1.3 Antisense Oligodeoxy-Nucleotides 75
1.4 Obstacles to Successful Targeted Therapyof Malignant Gliomas 76
2 Preclinical and Clinical Studies of Molecular Therapies in Malignant Gliomas 77
2.1 Targeting Receptor Tyrosine Kinase Signaling Pathways 77
2.1.1 Targeting the PDGF/PDGFR Signaling Pathway 77
2.1.2 Targeting the EGF/EGFR Signaling Pathway 83
2.1.3 Targeting the FGF/FGFR Signaling Pathway 84
2.1.4 Targeting the IGF/IGFR Signaling Pathway 84
2.1.5 Targeting Intracellular Signaling Pathways 84
2.2 Multitargeting Small Molecule Inhibitors 85
2.3 Antiangiogenic Treatment in Malignant Gliomas 88
2.3.1 Antiangiogenic Treatment Regimes Used in Malignant Gliomas 89
2.3.2 Effects of Antiangiogenic Treatment on Brain Tumor Edema 90
2.3.3 Evaluation of Brain Tumor Response to AntiangiogenicTherapy Approaches 90
2.3.4 Potential CNS Toxicity of Antiangiogenic Agents 92
2.4 Targeting TGF-Beta: Antisense Oligodeoxynucleotide Therapy Approaches of Malignant Gliomas 92
3 Conclusions and Future Directions 93
References 94
Novel Strategies for the Treatment of Brain Cancer 100
1 Introduction 101
2 Current Management of GBM 101
3 Molecular Pathomechanism of GBM as the Basis for Innovative Treatments 101
3.1 Signaling Pathways in GBM as Therapeutic Targets 102
3.2 Cancer Stem Cells and GBM 102
4 Innovative Strategies for the Treatment of GBM 103
4.1 Antiangiogenesis Approaches for Treatment of GBM 103
4.2 Innovations in Drug Delivery to GBM 107
4.2.1 Anticancer Agents with Increased Penetrationof Blood-Brain Tumor Barrier 107
4.2.2 Local Delivery of Chemotherapeutic Agents into the Tumor 108
4.2.3 Convection-Enhanced Delivery 109
4.2.4 Liposomes for Drug Delivery to GBM 109
4.2.5 Use of Nanoparticles for Drug Delivery to GBM 110
5 Personalized Management of GBM 110
5.1 Genetic/Genomic Basis for Personalizing Treatment of GBM 111
5.2 Molecular Diagnostics for Personalized Management of GBM 111
5.2.1 Diffusion MRI as a Biomarker 112
5.2.2 Combined Neuroimaging and DNA Microarray Analysis 112
5.2.3 Proteomics of GBM 112
5.2.4 Epigenetic Biomarkers of GBM 113
5.2.5 Personalized Chemotherapy of GBM 113
5.2.6 Molecular Determinants of Response to EGFR Inhibitors 113
5.2.7 Simulating Chemotherapeutic Schemes for Individualization 114
5.2.8 Personalized Therapy of GBM Based on Cancer Stem Cells 114
6 Limitations of Current Therapies for GBM 114
7 Future Prospects 115
References 116
Gene Therapy for Malignant Glioma 118
1 Introduction 119
2 The Transgenes 120
3 The Vectors 121
3.1 Viral Vectors 122
4 Oncolytic Vectors for Glioma 125
4.1 Enhancement of CRAd's Tropism for Brain Tumor Cells 126
4.1.1 Redesigning the Adenoviral Capsid to PromoteTransduction in Neoplastic Cells 126
4.1.2 Transcriptional Targeting of Viral Genes or Transgenes Using Tumor Specific Promoters 128
4.1.3 Deletion of Viral Genomic Regions that are not Required for Replication in Cancer Cells 129
5 Future Directions: Stem Cells Aid Gene and Oncolytic Therapy Vectors to Reach Distant Tumor Pockets on Infiltrating Gliomas 130
6 Conclusions 131
Acknowledgements 132
References 132
Immunotherapeutic Approach for Glioma by Alphaviruses as Positive Strand RNA Viruses 140
1 Introduction 141
2 RNA Viruses as Gene Expression Vectors 142
3 The Biology of Alphaviruses 142
4 Heterologous Gene Expression Using Alphavirus Vectors 143
5 Gene Therapy Strategies Using Alphavirus Vectors 144
5.1 Immunotherapeutic Approach 145
5.2 Replication-Competent Alphaviruses 149
6 Alphavirus Vector Development for Gene Therapy Application 149
7 Conclusions 151
References 152
Diagnosis of Brain Tumors Through Global Specific DNA Methylation Analysis 156
1 DNA Methylation 157
2 5-Methylcytosine as a Main Epigenetic Marker in DNA 158
3 Oxidative Damage of m5C 159
4 Methods of DNA Methylation Analysis 161
5 Epigenetic Method of 5-Methylcytosine Analysisin DNA from Different Tissues 162
5.1 Description of the Method 163
6 Analysis of 5-Methylcytosine in DNA of Patients with Brain Tumors 163
7 Analysis of 5-Methylcytosine in DNA of Patientswith Other Diseases 166
8 Aging 167
9 Conclusions 168
References 168
Molecular Markers of Gliomas 171
1 Introduction 172
1.1 Most Relevant Affected Pathways in Gliomas 173
2 Loss of Heterozygosity on Chromosome 1p and 19q 176
2.1 LOH on Chromosome 1p and 19q in ODs 176
2.2 LOH on Chromosome 1p and 19q in oligoastrocytomas 177
2.3 Partial Deletion on 1p 177
2.4 Clinical Relevance of LOH on Chromosome 1p and 19q 178
2.5 Genes Targeted by Deletions on 1p and 19q 178
3 LOH on Chromosome 10q and PTEN Mutations 179
3.1 LOH on Chromosome 10q and PTEN Mutations in Different Glioma Subtypes 179
3.2 Clinical Relevance of LOH on Chromosome 10q and PTEN Mutations 180
4 LOH on Chromosome 17p and P53 Mutations 181
4.1 LOH on Chromosome 17p and P53 Mutationsin Different Glioma Subtypes 181
5 EGFR 183
5.1 EGFR Amplification/Overexpression 183
5.2 Monoclonal Antibodies Against EGFR 183
6 O6-Methylguanine DNA Methyltransferase 185
6.1 MGMT Promoter Methylation Status in Different Glioma Subtypes 186
Note 187
7 CD133 187
References 187
Microarray and Proteomic Analysis of Gliomas: Target Strategies 192
1 Introduction 193
2 Background 194
2.1 Glioblastoma Multiforme 194
2.2 The Five Tools 194
3 Source of GBM Material for Target Identification Using Gene Expression Tools, Genomic Analyses, and Proteomic Analyses 195
3.1 Tumor Biopsies 195
3.2 Microdissection of GBM Cells 196
3.3 In Vitro Cultures of GBM Cells 196
3.4 Xenografted GBM Cells as a Source 197
3.5 Analysis of Recurrent Tumor Cells That Have BeenTreated with Radiotherapy and/or Temozolamide 198
4 Targets 198
5 Target Validation 200
6 Delivery Systems 202
6.1 Administration Validation 202
6.2 Adenoviral Vector Delivery System 202
6.3 Adeno-Associated Vector Delivery System 203
6.4 Poliovirus Vector Delivery System 204
6.5 Retroviral Vector Delivery System 204
6.6 Artificial Viral Particle Delivery System 204
6.7 Lipsomal, PLL or PEI In Vivo Gene Delivery 204
6.8 Local Electroporation 205
6.9 Direct Oligo-Nucleotide Delivery 205
7 Future Perspectives and Discussion 205
Acknowledgements 206
References 206
Nanosystems for the Delivery of RNAi 210
1 Introduction 211
1.1 Functional Analysis of Tumor-Relevant Genes in Brain Tumors Through Knockdown Approaches 211
2 RNA Interference 212
2.1 Discovery and Mechanism 213
2.1.1 The Initiation Phase: Dicer Mediates Cleavage of Long dsRNA 215
2.1.2 The Effector Phase: RISC-Mediated Cleavage of mRNA 215
2.2 siRNA and shRNA 216
2.2.1 Vector-Based RNAi 217
3 Delivery Strategies for siRNA and shRNA: General Considerations 217
3.1 Carriers for siRNA and shRNA Construct Delivery 218
3.2 Delivery Across the Blood-Brain Barrier 219
4 Systems for Local Application of siRNA/shRNA Constructs 220
5 Systemic Application of siRNA/shRNA Constructs 225
6 Outlook 227
References 228
Interference RNA Intervention in Brain Tumors 234
1 Introduction 235
2 Tenascin-C 237
3 Selected Molecular Targets for Brain Tumor Treatment 244
4 Current Anti-invasion Clinical Trials 249
5 RNA Interference for Tenascin-C Inhibitionin Brain Tumors 251
6 Perspectives 258
References 259
Blood-Brain Barrier Transport for RNAi 267
1 Introduction 268
2 Trojan Horse Liposome Technology 271
3 Brain Expression of shRNA RNAi Genes Using THL 271
4 In Vivo Silencing of Gene Expression in a Brain Tumor Model and Increased Survival Rate 274
5 In Vivo Delivery of SiRNA with Targeted MAbs and Avidin-Biotin Technology 277
6 Conclusions and Future Directions 280
References 282
Therapeutic Potential of Small Interfering RNA for Brain Diseases 286
1 RNA Interference 287
2 Spinocerebellar Ataxia and Other Polyglutamine-Associated Ataxias 290
3 Alzheimer's Disease 292
4 Parkinson's Disease 295
5 Amyotrophic Lateral Sclerosis 295
6 Multiple Sclerosis 297
7 Brain Tumors 299
8 Conclusions 302
References 302
RNA Interference-Based Therapies Against Brain Tumors: Potential Clinical Strategies 307
1 Introduction 308
1.1 RNA Interference: The Beginnings 309
1.2 The Expanding Family of Small RNAs and Their Widening Role in Cellular Functions 310
1.3 MicroRNA: The siRNA of the Genome 311
2 RNAi: The Mechanisms of Interference 312
2.1 siRNA and Its Mechanism of Interference 312
2.2 miRNA and Its Mechanism of Interference 314
3 The Design of siRNA for Preclinical Evaluation 314
3.1 The Evolving Rules for Rational siRNA Design 314
3.2 Minimizing Off-Target Effects of siRNA 314
3.3 Unintended Interactions Between Designed siRNA and 3 Untranslated Regions of ``Off-Target´´ mRNA 316
3.4 Which Strand is Selected as the Guide Strand? 316
4 Experimental Strategies 316
4.1 Experimental Strategies with siRNA 316
4.2 Experimental Strategies with miRNA 317
4.3 miRNA/siRNA Hybrids 318
4.4 In Vivo Imaging of RNAi Delivery 318
5 siRNA Targets in Glioma: Preclinical Studies 319
5.1 Targeting Glioma Cell-Surface Receptors via RNAi 319
5.1.1 The EGF Receptor 320
5.1.2 Formyl Peptide Receptor (FPR) 320
5.1.3 Ephrin Receptor 321
5.1.4 The Urokinase Plasminogen Activator Receptor (uPAR) 321
5.1.5 CXCR4 Receptor 321
5.1.6 Other Glioma Cell-Surface Receptors and Glioma Proteins Targeted by siRNA 321
5.2 Targeting Glioma Invasion via RNAi 322
5.3 Induction of Glioma Apoptosis via RNAi 323
5.4 Enhancing Chemo-sensitivity and Radiosensitivity via RNAi 323
5.5 Targeting Hypoxia-Induced Glioma Angiogenesis Cascades via RNAi 324
5.6 Targeting Glioma Metabolism via RNAi 324
5.7 Other Glioma Signaling Pathways Targeted by RNAi 325
5.8 siRNA Mediated Modulation of Immuno-Activity Against Glioma 325
5.9 Targeting Brain Tumor Stem Cells via RNAi 325
6 MicroRNA Targets in Glioma 326
7 Systemic Delivery of RNAi to Brain Tumors 326
8 RNAi in the Clinic: Current and Future Perspectives 327
9 Conclusions 328
Acknowledgements 328
References 328
MicroRNA: Biogenesis, Regulation, and Role in Primary Brain Tumors 336
1 Introduction 337
2 Genomic Organization of miRNA Loci 338
3 MiRNA Biogenesis 340
4 MiRNA Effector Mechanisms 341
5 Regulation of miRNA Expression and Function 343
6 MiRNA Detection and Quantification 344
7 In Vitro and In Vivo Modulation of miRNA Levels 348
8 MiRNAs in Cancer 349
9 MiRNA in Brain Tumors 350
9.1 Pituitary Adenomas 351
9.2 Medulloblastomas 351
9.3 Gliomas 355
10 Summary and Perspectives 357
References 357
Treatment of High-Grade Gliomas in Adults 364
1 Surgical Treatment of Newly Diagnosed Gliomas 365
2 Surgery for Recurrent Disease 367
3 Adjuvant Therapies at Resection 367
3.1 Carmustine Wafers 368
3.2 Convection-Enhanced Delivery 368
3.3 Interstitial Brachytherapy 369
3.4 Radioimmunotherapy 369
4 Radiotherapy 370
4.1 Adjuvant Radiotherapy 370
4.2 Radiosurgery 371
4.3 Proton Therapy 372
4.4 Radiation Sensitizers 372
5 Chemotherapy for Newly Diagnosed Gliomas 373
5.1 Nitrosoureas 373
5.2 Temozolomide 373
5.3 Pseudoprogression 375
6 Chemotherapy for Recurrent High-Grade Gliomas 375
6.1 Bevacizumab 376
7 Anaplastic Oligodendrogliomas and Oligoastrocytomas 376
7.1 PCV 377
7.2 Temozolomide 378
8 Investigational Therapies 378
8.1 Targeted Molecular Therapies 378
8.2 Anti-Angiogenic Treatments 381
8.3 Other Therapies 382
9 Conclusions and Future Directions 382
Acknowledgement 382
References 383
Treatment of Malignant Gliomas with Antisense Oligonucleotides 392
1 Introduction 393
1.1 Technique and Types of Oligonucleotides 393
1.2 Selection of Target Genes for Therapeutic Ablation Using Antisense ODN Strategy 396
1.3 Selection of Target Sequences for Therapeutic Ablation by a Antisense Oligonucleotides 397
2 Preclinical Approaches with Antisense ODNS in Gliomas 397
3 Clinical Studies with Antisense ODNs in Human Glioma Patients 399
3.1 In Vivo Targeting of Intracellular Signaling Pathways by a PKC-Alpha-Specific S-ODN (Affinitak) in Malignant Gliomas 400
3.2 In Vivo Targeting of Extracellular Receptor for IGF-1 in Human Malignant Gliomas 403
3.3 In Vivo Targeting of Toll-Like Receptor 9 by CpG-28 S-ODNs in Malignant Gliomas 404
3.4 In Vitro and In Vivo Development of TGF-Beta as Target for High-Grade Gliomas 405
4 Conclusion 409
References 410
Suppression of EGFR Expression by Antisense RNA and RNAi 415
1 Introduction 416
2 Construction of Antisense EGFR RNA and EGFR siRNA Expression Plasmids 417
3 Transfection of Antisense EGFR RNA and EGFR siRNA Expression Plasmids and Detection of EGFR Expression 418
4 Effects of Antisense EGFR RNA and EGFR siRNA on the Viability and Invasive Ability of U251 Cells In Vitro 419
5 Effects of Antisense EGFR RNA and EGFR siRNA on the Glioma Growth In Vivo 421
6 Discussion 424
Acknowledgement 429
References 429
Brain Tumor Therapy with Antisense Oligonucleotides 433
1 General Aspects 434
2 Targets for Antisense Oligonucleotides in Brain Tumor Therapy 435
2.1 Receptor Tyrosine Kinase c-Metc-Met 436
2.2 Ras/Raf-KinaseRas/Raf-Kinase 437
2.3 Oncogene Bcl-2Bcl-2 437
2.4 Insulin-Like Growth Factor Type IInsulin-like growth factor type I 438
2.5 Vascular Endothelial Growth FactorVascular Endothelial Growth Factor 439
2.6Epidermal growth factor receptor Epidermal Growth Factor Receptor 440
2.7 Telomerastelomerase 440
2.8 Protein Kinase C AlphaProtein Kinase C alpha 441
3 Antisense in Plasma 442
4 Unspecific, Nonantisense Effectsnon-antisense effects of AON Treatment 443
5 Antisense and BBB 444
6 Administration of Antisense for Brain Tumor Therapy 445
6.1 Delivery of AON by Liposomesliposomes 445
6.2 AON Attached to Nanoparticlesnanoparticles 446
6.3 Direct Administration into the Cerebro-Spinal-Fluid 448
6.4 Administration via Convection-Enhanced Deliveryconvection enhanced delivery 449
6.5 Antisense as Intranasal Drug 450
7 Antisense Against TGF-beta2 451
8 Antisense for Other Immunological Approachesimmunological approaches 452
9 Conclusion 453
References 453
Noncoding RNAs in the Development, Function and Pathologies of the Central Nervous System 460
1 Introduction 460
2 Regulatory RNAs 461
2.1 NcRNAs in Epigenetic Regulation 463
2.2 NcRNAs in the Regulation of Transcription 464
2.3 NcRNAs in Posttranscriptional Regulation 465
3 NcRNAs in the Development of Nervous System 466
4 Noncoding RNAs in Diseases Affecting the Nervous System 468
4.1 Neurological Diseases 468
4.2 Brain Cancer Tumors 470
5 NcRNAs as Therapeutic Targets 472
References 473
The Non-Coding Oncofetal H19 Gene in Brain Tumors 478
1 H19: An Imprinted Non-coding RNA Gene 480
2 H19 and IGF2 in Developing and Adult Brain 480
3 H19 Tumorigenic Properties are Reactivated During Various Stages of Tumor Development 481
4 H19-IGF2 Locus and Brain Tumors 483
5 Hypoxia and p53 Mutations, Which are Hallmarks of Astrocytomas are Known Determinants of H19 Expression 484
6 H19-DTA/H19-DTA-P4-DTA and H19-siRNAs-Putative Therapeutic Agents Against Brain Tumors 487
References 489
Index 492