Essentials of Apoptosis (eBook)

Preface to Second Edition 5
Preface to First Edition 7
Contents 7
Contributors 12
Color Plates 19
Part 1: Molecules and Pathways of Apoptosis 25
Caspases: Activation, Regulation, and Function 26
Introduction 26
Caspases-A Historical Perspective 28
Activation of Caspases 29
Activation of Apoptotic Executioner Caspases 29
Apoptotic Activation Platforms 32
Activation of Apical Caspases 33
Other Activation Platforms and Their Caspases 34
Caspase Inhibitors 37
Caspase Substrates 39
Conclusion 41
Abbreviations 41
References 41
The Bcl-2 Family Proteins 48
Introduction 48
Evolutionary Conservation of Bcl-2 Family Proteins 49
Bcl-2 Family Protein Interactions and Their Functional Significance 53
Protein Interactions Among Bcl-2 Family Members 53
The Importance of BH Domains in Bcl-2 Family Protein Interactions 55
Interactions Between Bcl-2 Family Proteins and Other Molecules 56
Regulation of the Bcl-2 Family Proteins by Nonfamily Molecules 56
Participation in Multiple Functions via Binding to Different Molecules 58
The Crystal and Solution Structures of the Bcl-2 Family Proteins 59
Regulation of the Bcl-2 Family Proteins 61
Regulation of Expression 61
Regulation Through Alternative Splicing 62
Regulation Through Posttranslational Modifications 62
Change of Subcellular Locations Resulting from Posttranslational Modifications 62
Change of Functions Resulting from Posttranslational Modifications 64
Molecular Mechanisms of the Control of Apoptosis by the Bcl-2 Family Proteins 65
Activation of the Multidomain Bax and Bak at the Mitochondria 65
Regulation of Apoptosis at the Endoplasmic Reticulum 69
The Physiological Roles of the Bcl-2 Family Proteins 69
Role in the Regulation of Apoptosis 70
Role in the Regulation of Autophagy 71
Role in the Regulation of Cell Proliferation 72
Role in Other Physiological Functions 72
Role of the Bcl-2 Family Proteins in Cancer Biology and the Development of BH3-Based Therapeutic Strategies 73
Concluding Remarks 75
References 75
The Mammalian IAPs: Multifaceted Inhibitors of Apoptosis 85
Introduction 85
IAP Proteins: Multifaceted Inhibitors of Apoptosis 88
Inhibition of Caspase Function 88
Inhibition or Promotion of Caspase Activity Through Ubiquitination and Degradation of Caspases or IAPs 91
Modulation of Survival Signal Transduction Pathways 92
Negative Regulation of the IAPs 96
Smac/DIABLO: An IAP Antagonist and a Caspase Activator 96
Other IBM-Containing Proteins as Potential IAP Antagonists 99
XAF1 Is an Interferon-Inducible IAP Antagonist and a Candidate Tumor Suppressor 99
Summary: Regulation of Apoptosis by the IAPs 100
The IAPs in Health and Disease 102
Biological Roles of the IAPs: Evidence from Animal Gene Ablation Studies 102
Pathological Roles of the IAPs in Cancer 103
IAP Dysfunction in Human Diseases Other Than Cancer 103
Conclusions 107
References 108
Structural Biology of Programmed Cell Death 116
Introduction 116
Death Receptors 117
Bcl-2 Family of Proteins 119
Caspases-The Executioners of Apoptosis 122
Inhibitors of Apoptosis (IAP) 125
Caspase-IAP Complex 126
Caspase-p35 Complex 128
Smac/DIABLO 128
Smac-IAP Complex 128
Signaling Modules in Apoptosis 133
Apoptosome and the Activation of Initiator Caspases 134
Conclusion 136
References 136
The Death Receptor Pathway 140
Introduction 140
Fas (CD95/APO-1) and Fas Ligand (FasL/CD95L) 144
Fas (CD95/APO-1) 144
Fas Ligand (FasL/CD95L) 145
Fas Signaling 145
Physiology and Pathophysiology 148
Tumor Necrosis Factor-Receptor 1 (TNF-R1) and TNF-alpha 150
TNF-R1 150
TNF-alpha 151
TNF-R1 Signaling 151
Physiology and Pathophysiology 153
TRAIL Receptors and TRAIL 156
TRAIL Receptors 156
TRAIL 158
TRAIL-R1 and TRAIL-R2 Signaling 158
Physiology and Pathophysiology 160
Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD) and APO-3L 161
Death Receptor 6 (DR6) 161
Experimental Tools for Inhibiting Death Receptor-Mediated Apoptosis 162
Conclusions 163
References 164
The Mitochondrial Pathway: Focus on Shape Changes 172
Mitochondria 172
Mitochondria and Apoptosis 173
Mechanisms of Cytochrome c Release 175
Changes in Mitochondrial Shape During Apoptosis 177
Regulation of Mitochondrial Morphology 177
Pro-fusion 177
Pro-fission 179
Proteolytic Control of Mitochondrial Shape 179
Which Physiological Role for Mitochondrial Morphology? 181
Changes in the Internal Shape of Mitochondria 182
Changes in the Mitochondrial Reticulum 183
Mammals 184
Yeast 185
C. elegans 186
Drosophila 187
Functional Consequences 187
Conclusions: Which Role for Mitochondrial Shape Changes in Apoptosis Associated with Disease? 188
References 190
The Endoplasmic Reticulum Pathway 197
Introduction 197
The Unfolded Protein Response 198
ER Chaperones 200
ER Stress and Autophagy 201
Apoptosis Pathways 202
Calcium Signaling and Apoptosis 203
Regulation of Calcium Signaling by Bcl-2 206
Regulation of Calcium Signaling by Bax and Bak 207
BH3-Only Proteins 208
Conclusion 209
References 210
Reactive Oxygen Species in Cell Fate Decisions 218
Introduction 219
Cellular Sources of ROS 219
NADPH Oxidase (NOX) and ROS 220
Mitochondrial ETC as the Source of ROS 220
Mitochondria as Targets of ROS in Apoptosis 221
Regulatory Role of ROS in Death Receptor-Mediated Apoptosis 223
ROS in TNFR1-Mediated Apoptosis 223
Involvement of ROS in CD95-Mediated Apoptosis 224
ROS and TRAIL-Mediated Apoptosis 224
Redox Regulation of JNK and NF-kappaB 223
Redox Regulation of JNK During Apoptotic Signaling 225
Regulation of NF-kB During ROS-Mediated Apoptosis 227
ROS as Messengers Between NF-kappaB and JNK in TNFalpha-Induced Cell Death 228
The Other Faces of ROS 223
Pro-life and Proliferative Activity of ROS 230
Apoptosis Inhibition: O2.- or H2O2? 231
Superoxide as the Oncogenic Signal of Bcl-2 233
Intracellular pH as a Potential Target of ROS 233
Concluding Remarks 234
References 235
The Integration of Metabolism and Cell Death 241
A Shared Platform: The Mitochondria 241
Apoptosis Is an Energy-Dependent Process 242
The PI3K/Akt Pathway 243
Nutrient Deprivation and Cell Death 245
Metabolic Regulation of Apoptotic Machinery 247
Regulation of Metabolism by Apoptotic Proteins 248
New Metabolic Roles for Old Proteins: p53 249
The Warburg Effect and Cancer: Bringing It All Together 250
References 251
Transcriptional Regulation of Apoptosis 256
Introduction 256
Regulation of Genotoxic Stress-Induced Apoptosis by the p53 Family and AP-1 258
Apoptotic Response to Genotoxic Stress 258
The p53 Family Proteins 258
Apoptosis Mediated by p53 258
Apoptotic Targets of p73 and p63 261
AP-1 Family 261
AP-1 in Apoptosis Regulation 262
Other Transcription Factors in Genotoxic Stress-Induced Apoptosis 262
Regulation of Oncogenic Stress-Induced Apoptosis by E2F and MYC 263
Oncogenic Stress-Induced Apoptosis 263
Apoptosis Mediated by E2F 263
Apoptosis Induced by Myc 265
Regulation of Cytokine- and Growth Factor Withdrawal-Induced Apoptosis by NF-kappaB, IRF-1, STAT, and FOXO 266
Cytokine- and Growth Factor Withdrawal-Induced Apoptosis 266
NF-kappaB and Apoptosis 266
Apoptosis Mediated by IRF-1 267
STAT and Apoptosis 268
Apoptosis Mediated by FOXO 269
Regulation of Developmental Apoptosis by HOX and Snail 269
Apoptosis in Development 269
Apoptotic Targets of HOX 270
Snail in Apoptosis Regulation 271
Conclusions 271
References 271
Clearance of Apoptotic Cells - Mechanisms and Consequences 278
Cell Death and Clearance 278
The Clearance Process: Migration Toward Dying Cells 279
The Clearance Process: Recognition of Dying Cells 280
The Clearance Process: Engulfment of Dying Cells 284
The Clearance Process: Digestion 285
Inflammatory Mediator Production Following Apoptotic Cell Uptake 287
T-Cell Activation Following Apoptotic Cell Uptake 289
Failed Clearance and Autoimmunity 290
Exploitation of Apoptotic Cells by Tumors and Pathogens 291
References 293
Systems Biology Approaches to the Study of Apoptosis 300
Introduction 300
Deterministic Modeling of Apoptotic Signaling 302
Stochastic Modeling of Apoptotic Signaling 307
Spatial Modeling of Apoptotic Signaling 308
Bistability of Apoptotic Signaling Networks 309
Statistical Models of Apoptotic Signaling 310
Current and Future Challenges in Systems Modeling 310
References 310
Part 2: Apoptosis in Model Organisms 315
Programmed Cell Death in Plants: Apoptotic but Not Quite 316
Introduction 316
Morphological Changes During Plant PCD 318
Mediators of PCD Signals in Plants 321
Reactive Oxygen Species (ROS) as Effector and Mediator 321
Role of Salicylic Acid 322
Involvement of Calcium and Its Related Signaling 323
Modulation of PCD by Lipid-Related Signals 324
Mechanisms for PCD Activation: The Role of Proteases and Core Regulators in Plant PCD 325
The Role of Proteases 325
Caspase-Like Proteases 325
Vacuolar Processing Enzyme (VPE) 326
Metacaspases 327
Saspases 328
Other Proteases 329
Role of Core Regulators in Plant PCD 329
BAX Inhibitor-1 329
BON and BAP Families 331
BAG Protein Family 331
Future Perspectives 332
References 333
Tracing the Roots of Death: Apoptosis in Saccharomyces cerevisiae 340
Introduction 340
The Routes to Death-Triggering Yeast Apoptosis 341
Exogenous Induction of Yeast Programmed Cell Death 341
Hydrogen Peroxide and Acetic Acid 341
Other External Triggers: Drugs, Toxins, Metals, and Radiation 342
Heterologous Expression of Apoptosis Modulators 344
Endogenous Induction of Yeast Programmed Cell Death 345
Mutation-Induced Deregulation of Cellular Homeostasis 345
Aging 346
Replicative Aging 346
Chronological Aging 347
Chronological Versus Replicative Aging: Differences and Crossroads 347
Autophagy and Cell Death: Companions or Competitors? 348
The Roots of Death-Mapping the Molecular Machinery 349
Small Molecules as Mediators 350
Proteasome and Proteases 350
Mitochondrial Factors: Toxic When Released 352
The Roofs of Death-Physiological Sense and Medical Implications 354
Physiological Sense 354
Medical Implications 356
Rooms for Death-Apoptosis in Other Unicellular Organisms 357
Fungi 357
Schizosaccharomyces pombe 357
Candida albicans and Other Pathogenic Fungi 357
Protozoan Parasites 358
Conclusions 358
References 359
Programmed Cell Death in C. elegans 370
C. elegans as a Model Organism for Studies of Programmed Cell Death 370
The Genetic Pathway for Programmed Cell Death 372
Activation of Cell Death 373
The Genetic Pathway for Cell Killing 373
Molecular Identities of egl-1, ced-3, ced-4, and ced-9 374
Molecular Model for the Killing Process 374
Structural Analysis of CED-4, CED-9, and EGL-1 376
Specification of the Life vs. Death Fates 377
HSN Neurons 377
Sister Cells of NSM Neurons 377
CEM Cell Fate Specification 378
Engulfment of Cell Corpses 379
Two Partially Redundant Signaling Pathways Promote Cell Corpse Engulfment 379
Externalized PS as an ‘‘Eat-Me’’ Signal and the PS Externalization Process 381
Internalization and Degradation of Apoptotic Cells 382
Degradation of Chromosomal DNA in Dying Cells 383
Summary 384
References 385
Cell Death in Drosophila 389
Introduction 389
Cell Death Pathways 390
The Apoptotic Machinery 390
Extrinsic Signals for Caspase Activation 393
Tools of the Trade: How We Observe and Block Apoptosis in Drosophila 394
Observing Apoptosis 394
Blocking Apoptosis 395
Early Use of Cell Death in Oogenesis and Embryogenesis 395
Cell Death in Drosophila Oogenesis 395
Cell Death in the Embryonic Epidermis 396
Death in the CNS 398
Embryonic Head Development 398
Cell Death Prior to and During Metamorphosis: The Mechanism of Cell Death Depends on the Larval Tissue Type 399
Autophagic Cell Death in Midgut and Salivary Gland Histolysis 400
Examples of Classical Apoptosis 401
Larval Wing Disc 402
The Pupal Notum 402
The Developing Eye 403
Cell Death in the Larval Eye Disc 403
Cell Death in the Pupal Eye 405
Cell Death in the Newly Emerging Adult 406
Degeneration in Adults 407
Compensatory Proliferation 408
Demolishing or Remodeling? The Apoptotic Machinery in Nonapoptotic Processes 409
Summary 410
References 411
Part 3: Apoptosis in Mammalian Physiology and Pathogenesis 420
Cell Death: Defining and Misshaping Mammalian Embryos 421
A Bit of History 421
Cell Death in the Germ Line 422
Cell Death in the Cleaving Embryo 423
Cell Death During Organogenesis 424
Consequences of Deregulation of Cell Death 425
Conclusions and Summary 431
References 431
Matters of Life and Death in the Immune System 435
Introduction 435
Apoptosis Pathways 436
T-Cell Development 436
Peripheral Maintenance and Tolerance 440
T-Cell Memory 441
CD8 Effector Function 441
Regulatory T-Cell Function 442
B-Cell Development 443
Apoptosis in Myeloid Cells 444
Apoptotic Cells Induce Tolerance 446
Nonapoptotic Roles for Apoptosis Genes in the Immune System 447
Concluding Remarks 448
References 448
Cell Death in the Hematopoietic System 455
Introduction 455
Hematopoietic Stem Cells 457
Neutrophils 459
Macrophages 461
Megakaryocytes and Platelets 462
Erythrocytes 464
Conclusions 466
References 466
Cell Death in Acute Neuronal Injury 472
Introduction to Cell Death in Acute Neuronal Injury 472
Morphology of Acute Neuronal Injury 473
Necrosis, Apoptosis, Autophagy, or All of the Above? 473
Not All Neurons Are Created Equal 476
Cell Death Execution in Acute Neuronal Injury 477
Cell Death Signaling in Acute Neuronal Injury 479
Cell Death and Clinical Tools 482
References 483
Apoptosis in Neurodegenerative Diseases 490
Introduction 490
Apoptosis in Alzheimer’s Disease 491
Apoptosis in Parkinson’s Disease 494
Apoptosis in HD 496
Conclusion 498
References 502
Apoptosis in Cardiovascular Pathogenesis 516
Introduction 516
The Cardiac Apoptotic Pathways 519
Regulation of Apoptosis 521
Therapeutic Implications 525
References 528
Apoptosis in Lung Injury and Disease 533
Introduction 534
Apoptosis in Acute Lung Injury 536
Oxidative Lung Injury 537
Pulmonary Cell Death in Hyperoxia 539
Epithelial Cell Responses 539
Alveolar Macrophages 540
Fibroblasts 540
Endothelial Cells 540
Ventilator-Induced Lung Injury 541
Lung Ischemia-Reperfusion Injury 542
Lung Cell Death in Hypoxia/Reoxygenation Injury 542
Apoptosis in the Pathogenesis of Chronic Obstructive Pulmonary Disease 543
Cigarette Smoke Exposure 545
Other Emphysema Models 547
Pulmonary Hypertension 548
Fibrosis 548
Conclusions and Therapeutic Strategies 549
References 550
Apoptosis in Liver Injury and Liver Diseases 556
Death Receptor-Mediated Liver Injury 558
Viral Injury 561
Alcoholic Liver Injury 562
Nonalcoholic Steatohepatitis 563
Autoimmune Hepatitis 564
Cholestatic Liver Injury 564
Drug-Induced Liver Injury 565
Ischemia-Reperfusion Injury 565
Hepatocellular Carcinoma (HCC) 566
Summary 566
References 567
Apoptosis in Acute Kidney Injury 574
Introduction 574
Apoptosis in Ischemic AKI and Cisplatin Nephrotoxicity 575
Apoptotic Pathways Activated During Ischemic AKI and Cisplatin Nephrotoxicity 576
Apoptotic Pathways in Ischemic AKI 576
Apoptotic Pathways Activated During Cisplatin Nephrotoxicity 577
Upstream Triggers of Apoptosis in Ischemic and Cisplatin Nephrotoxic AKI 579
Apoptotic Triggers in Ischemic Renal Injury 579
Energy Depletion 579
Disturbance in Ion Homeostasis 579
Reactive Oxygen Species (ROS) Accumulation 579
Inflammation 580
Induction and Activation of Apoptotic Genes 580
Upstream Events Leading to Tubular Cell Apoptosis During Cisplatin Nephrotoxicity 581
ROS 581
DNA Damage 581
CDK2-p21 Pathway 582
Inflammation 582
Inhibition of Apoptosis for the Prevention and Treatment of AKI 583
References 584
Apoptosis in Cancer Biology and Cancer Therapeutics 589
Introduction 589
Apoptosis Pathways 590
Apoptosis and Cancer Biology 590
Defects in the Death Receptor Pathway in Human Cancers 591
Defects in the Mitochondrial Pathway in Human Cancers 592
Apoptosis and Cancer Therapy 593
Cancer Therapeutics Targeting the Death Receptor Pathway 594
Cancer Therapeutics Targeting Bcl-2 Family Proteins 596
Cancer Therapeutics Targeting Inhibitor-of-Apoptosis Proteins 597
Conclusions 598
References 599
Part 4: Alternative Cell Death Mechanisms and Pathways 605
Necrosis: Molecular Mechanisms and Physiological Roles 606
Introduction 607
Physiological and Pathological Significance of Necrotic Cell Death 608
Regulated Necrotic Cell Death 610
Death Receptor-Induced Necrotic Signaling 610
TLR- and NLR-Induced Necrotic Signaling 611
DNA Damage and Hydrogen Peroxide-Induced Necrotic Signaling 612
Mediators of Necrotic Cell Death 613
Calcium 613
Reactive Oxygen Species (ROS) 615
ROS Generation and Necrosis 616
ROS-Mediated Damage of Biomolecules 617
Phospholipases and Lipoxygenases 618
Proteases 619
Ceramide 621
Methylglyoxal 621
Innate Immune Response Following Necrotic Cell Death 623
Molecular Interference with Pathology-Associated Necrotic Cell Death 623
Concluding Remarks 626
Abbreviations 628
References 629
Caspase-Independent Mitotic Death 641
Introduction 641
Aneuploidy or Cell Death Occurs When the Spindle Checkpoint Fails 643
CIMD as Programmed Cell Death 645
Low Levels of BUB1 Are Required for CIMD 646
Autophagy Occurs During CIMD 646
Other Types of Mitotic Cell Death 647
CIMD and Tumorigenesis 648
Potential Targets of Cancer Therapy 649
Determination of the Spindle Checkpoint Activity by Monitoring Mitotic Index Can be Ambiguous 650
References 650
Lysosomal Proteases in Cell Death 653
Introduction 653
Nature of the Signals Leading to Lysosome-Induced Cell Death 654
Intracellular Mechanisms of Lysosomal Cell Death Induction 656
Receptor-Mediated Endocytosis 656
Lysosomal Membrane Permeabilization 657
How to Induce Lysosomal Membrane Permeabilization 658
Lysosomal Proteases 659
Nature of Proapoptotic Lysosomal Proteases 659
Cysteine Cathepsins 660
Cathepsin B 660
Cathepsin C 661
Cathepsin L 661
Aspartyl Cathepsins 662
Other Proteases 663
How Are Lysosomal Proteases Connected to Classical Apoptotic Pathways? 664
Therapeutic Implications 665
Can Tumor Progression Be Modulated via Lysosomal Proteases? 665
Role of Lysosomal Proteases in Neurodegenerative Diseases 666
Conclusion 666
References 667
Autophagy and Cell Death 676
Introduction 677
Basic Autophagy Machinery 677
Activation of Autophagy 679
Functional Roles of Autophagy in Mammalian Cells 681
Autophagy in the Regulation of Cell Death 681
Autophagy Promotes Cell Survival 682
Autophagy Can Participate in Cell Death 684
Factors That May Affect Whether Autophagy Presents a Prosurvival or Prodeath Effect 685
The Potential Clinical Significance of Modulating Autophagy to Control Cell Death 688
Conclusion 688
References 689
Part 5: Approaches to the Study of Apoptosis 694
Determination of Cell Viability 696
Introduction 696
General Procedures 696
Measurement of Plasma Membrane Integrity by Vital Dye Exclusion Assay 696
Measurement of Cytosolic Leakage 696
Clonogenic Activity 697
Comments 697
Morphological Examination 698
Introduction 698
General Procedures 698
Comments 699
Alterations in the Plasma Membrane 699
Introduction 699
General Procedures 699
Comments 700
Changes in the Cytosol 700
Introduction 700
Caspases 701
General Procedures 701
Western Blot for Detecting Caspase Cleavage and Caspase Substrate Cleavage 701
Measurement of Caspase Activities Using Synthetic Substrates 701
Measurement of Caspase Activation by Immunostaining or with Fluorescent Substrates in Tissues and Cells 702
Comments 703
Bcl-2 Family Proteins 703
General Procedures 703
Comments 704
Mitochondrial Changes 704
Introduction 704
Mitochondrial Release of Cytochrome c 705
General Procedures 705
Subcellular Fractionation 705
Western Blot Analysis 706
ELISA 706
Immunostaining 706
Comments 706
Mitochondrial Transmembrane Potentials 707
General Procedures 707
Comments 708
Changes in the Nucleus 708
Introduction 708
Nuclear Condensation and Fragmentation 709
General Procedures 709
Comments 709
DNA Content Staining by Propidium Iodide 709
General Procedures 709
Comments 710
DNA Fragmentation 710
Internucleosomal DNA Cleavage 710
General Procedures 710
Comments 711
Detection of DNA Breaks by Histochemical Methods (TUNEL) 711
General Procedures 711
Comments 711
Resources for Apoptosis Research 712
References 713
Index 716