Molecular Pathology of Lung Diseases (eBook)

Series Preface 6
Preface 8
Table of Contents 9
Contributors 14
Section 1 Basic Concepts of Molecular Pathology 21
1 Genes, Gene Products, and Transcription Factors 22
Introduction 22
Nucleic Acids, Genes, and Gene Products 22
Posttranslational Modifications of Gene Products 24
Phosphorylation and Acetylation 24
Protein Degradation and Ubiquitinylation 24
Transcription Factors 24
References 25
2 Receptors, Signaling Pathways, Cell Cycle, and DNA Damage Repair 30
Cell Surface Receptors and Signal Transduction 30
Signaling Pathways 30
The Cell Cycle 32
DNA Damage Repair 33
References 34
3 Cell Adhesion Molecules 41
Introduction 41
Integrins 41
a3ß1-Integrin and Small Cell Lung Carcinoma 42
CXCR4 Chemokine Receptors 42
Cyclooxygenase-2 42
Focal Adhesion Kinase 43
Other Integrin-Related Research 43
Cadherins 44
E-Cadherin 44
Cadherins and Cyclooxygenase-2 45
Cadherins and Epidermal Growth Factor Receptor 45
H-Cadherin 46
Other Cadherin-Related Research 46
Selectins 48
Immunoglobulin-Like Cell Adhesion Molecules 49
CD44 51
Conclusion 52
References 52
4 Apoptosis and Cell Death: Relevance to Lung 59
Introduction 59
Apoptosis and Other Forms of Cell Death 59
Necrosis 59
Autophagy 60
Paraptosis 61
Autoschizis 61
Apoptosis 61
Mechanisms of Apoptosis 61
Caspases 61
Extrinsic Death Pathway 62
Intrinsic Death Pathway 63
Regulators of Caspases 64
Adapter Proteins 64
The Bcl-2 Family of Proteins 65
Inhibitors of Apoptosis Proteins 65
Other Regulators 66
Protein Targets of Caspases 66
Apoptosis and the Pathogenesis of Lung Diseases 66
Acute Lung Injury/Acute Respiratory Distress Syndrome 66
Chronic Obstructive Pulmonary Disease 67
Asthma 67
Pulmonary Fibrosis 67
Lung Cancer 67
Conclusion 67
References 68
5 Roles of Mutation and Epimutation in the Development of Lung Disease 72
Introduction 72
Pathogenesis of Lung Disease 72
Mutations and Epimutations 72
Genetic Alterations 72
Epigenetic Alterations 73
Neoplastic Lung Diseases 73
Pathogenesis of Lung Cancer 73
Chromosomal Alterations in Lung Cancer 73
Amplification of the c-Myc Protooncogene in Lung Cancer 74
Common Chromosomal Deletions in Lung Cancer 74
Complex Chromosomal Rearrangements in Lung Cancer 74
Gene Mutations in Lung Cancer 75
The ras Gene Family 75
Tumor Suppressor p53 75
Tumor Suppressor p16INK4A 75
Epimutations in Lung Cancer 75
Obstructive Lung Diseases 76
Pathogenesis of Emphysema 76
Gene Mutations in Emphysema 76
Pathogenesis of Cystic Fibrosis 76
Gene Mutations in Cystic Fibrosis 76
Epimutations in Cystic Fibrosis 77
References 77
Section 2 Techniques and Experimental Systems in Molecular Pathology 81
6 Bioinformatics and Omics 82
Introduction 82
Bioinformatics 82
Omics 82
Genomics 82
Transcriptomics 82
Proteomics 83
Metabolomics 83
DNA Microarrays 83
Conclusion 83
References 83
7 General Approach to Molecular Pathology 87
Introduction 87
Nucleic Acid Extraction 87
Amplification Technologies 88
Target Amplification 88
Polymerase Chain Reaction 88
Other Target Amplification Techniques 89
Signal Amplification 89
Restriction Fragment Analysis and Southern Blotting 91
Restriction Fragment-Length Polymorphism 91
Southern Blotting 91
Sequencing 91
Sanger Sequencing 91
Real-time Sequencing 92
Advanced Sequencing 92
Methylation Detection Methods 92
Fluorescence In Situ Hybridization and Microarrays 92
Fluorescence In Situ Hybridization 92
Chromosomal Microarrays 92
Oligonucleotide Microarrays 93
Liquid Bead Microarrays 93
Mass Spectrometry 93
Systems Biology Approaches 93
Implementing Molecular Pathology 94
Laboratory Design Considerations 94
Laboratory Staffing 94
References 94
8 Applications of Molecular Tests in Anatomic Pathology 95
Introduction 95
Anatomic Pathology Testing to Detector Characterize Neoplasia 96
Oncogenes 96
Tumor Suppressor Genes 97
Molecular Anatomic Testing for Targeted Therapies in Lung Cancer 97
Anatomic Pathology Testing forInfectious Agents 97
References 98
9 Polymerase Chain Reaction and Reverse Transcription–Polymerase Chain Reaction 100
Polymerase Chain Reaction 100
Theory 100
Principles 100
Practical Polymerase Chain Reaction 103
Denaturation Step Programming 103
Annealing Step Programming and Primer Design 103
Polymerase Chain Reaction Components 104
Thermostable Polymerase 104
Deoxynucleotides 104
Polymerase Chain Reaction Buffer 105
Magnesium 105
Polymerase Chain Reaction Set-Up 105
Postprocedure Analysis 105
Variations 106
Real-Time Polymerase Chain Reaction 106
Reverse Transcription 109
References 111
10 Array Comparative Genomic Hybridization in Pathology 114
Principle of Comparative Genomic Hybridization 114
Array Comparative Genomic Hybridization Platforms 114
Arrays Based on Clone Inserts 114
cDNA Arrays 114
Large-Insert Clone Arrays 114
Repeat-Free and Nonredundant Sequence Arrays 116
Oligonucleotide Arrays Using Presynthesized Oligonucleotides 117
Oligonucleotide Arrays Based on In Situ Synthesis 117
General Platform Considerations 117
DNA Preparation and Hybridization 118
DNA Isolation and Quality 118
Microdissection and DNA Amplification 118
Reference DNA 119
DNA Labeling 120
Hybridization 120
Data Analysis 120
Image Processing 121
Background Subtraction 121
Normalization 121
Identifying an Aberration 121
Conclusion 122
References 123
11 Loss of Heterozygosity in Lung Diseases 125
Introduction 125
What Is Loss of Heterozygosity? 125
Detecting Loss of Heterozygosity 125
Tobacco Smoke and Loss of Heterozygosity 126
Other Factors Influencing Loss of Heterozygosity 126
Asbestos 126
Pathogens 126
Patterns of Loss of Heterozygosity in Lung Cancer 127
Loss of Heterozygosity at 1p 128
Loss of Heterozygosity at 3p 128
Loss of Heterozygosity at 5q 128
Loss of Heterozygosity at 8p 128
Loss of Heterozygosity at 9p 129
Loss of Heterozygosity at 10q 129
Loss of Heterozygosity at 13q 129
Loss of Heterozygosity at 15q 129
Loss of Heterozygosity at 17p 129
Loss of Heterozygosity at 19p 129
Loss of Heterozygosity on the X Chromosome 129
Loss of Heterozygosity in Benign Lung Diseases 130
Idiopathic Pulmonary Fibrosis 130
Sarcoidosis 130
Chronic Obstructive Pulmonary Disease and Asthma 130
Conclusion 130
References 130
12 In Situ Hybridization: Principles and Applications for Pulmonary Medicine 134
Introduction 134
In Situ Hybridization:General Principles 134
DNA Composition and Structure 134
Principles of Base Pairing 134
Denaturation, Renaturation, and Influencing Factors 135
Probes 136
Types of Probes 136
Chromosome Enumeration Probes 136
Locus-Specific Probes 137
Telomeric Probes 137
Chromosomal Paints 137
Probe Preparation 137
Directly Labeled Probes 137
Indirectly Labeled Probes 137
In-House Developed Probes 137
Fluorescence In Situ Hybridization 137
Procedure 137
Specimens 139
Prehybridization 139
Denaturation and Hybridization 139
Removing Nonspecifically Bound Probe 139
Fluorescence Microscopy 140
Chromogenic In Situ Hybridization 140
Other Techniques That Utilize In Situ Hybridization 141
Comparative Genomic Hybridization 141
Multicolor Whole-Chromosome Painting 142
Clinical Applications 143
Oncology 143
Tumor Detection 143
Tumor Typing 143
Prognostication and Guiding Treatment 144
Infectious Disease 144
Inherited Diseases 144
Conclusion 144
References 145
13 Proteomics 147
Omics 147
Genomics and Transcriptomics 147
Proteomics 147
Proteomics: A New Diagnostic Tool for Lung Diseases 148
The Ideal Proteomics 148
Shotgun and Protein Profiling 148
Protein Identification 149
Data Validation 149
Proteomics Instrumentation 149
Two-Dimensional Gel Electrophoresis 149
Methodologic Obstacles of PAGE 149
Protein Staining 150
Enzymatic and Nonenzymatic Digestion 150
Mass Spectrometry 151
Matrix-Assisted Laser Desorption/Ionization 151
Imaging Mass Spectrometry 151
Surface-Enhanced Laser Desorption/Ionization Mass Spectrometry 152
Other Types of Spectrometry 152
A “Dream Team” Mass Spectrometry System 152
Proteomics Protocols 153
Protein Identification 153
Mass Fingerprinting Identification 153
Sequence-Based Identification 153
Database Searching 154
Validation of Protein Match 154
Protein Quantification 155
Detection of Posttranslational Modification 155
Protein Complexes and Protein Interactions 156
Applications to Pulmonary Pathology 156
Noninfectious Inflammatory Diseases of the Lung 156
Infectious Diseases of the Lung 157
Transplant Rejection Versus Infection 157
Neoplastic Diseases of the Lung 157
References 159
14 Animal Models of Lung Disease 161
Introduction 161
Transgenic Mouse Models 161
Nonneoplastic Diseases 161
Chronic Bronchitis and Emphysema 161
Asthma 162
Cystic Fibrosis 162
Interstitial Lung Diseases 162
Animal Models of Lung Cancer 163
Knockout Mouse Models 163
Animal Models of Mesothelioma 164
Conclusion 164
References 164
15 Tissue Culture Models 167
Introduction 167
History of Tissue Culture 167
Types of Tissue Culture 168
Advantages and Limitations of Tissue Culture 169
Cell Culture and the Study of Disease Processes 169
Biology of the Cultured Cell 169
Culture Environment 169
Cell Adhesion 170
Development of Continuous Cell Lines 170
Dedifferentiation 170
Functional Environment 170
Lung Tissue Cell Lines: Establishment and Significance 171
Normal Human Bronchial Epithelial Cells 171
Pulmonary Endothelial Cells 171
Airway Smooth Muscle and Asthma 172
Lung Cancer Tissue and the Development of Novel Therapeutics 172
Infectious Diseases 173
Human Type II Alveolar Pneumocytes and Acute Lung Injury/Acute Respiratory Distress Syndrome 173
Three-Dimensional Biology 173
Conventional Bioreactors and Three-Dimensionality: The Origins of Three-Dimensional Culture 173
Three-Dimensional Models for Physiological Study 175
Three-Dimensional Models of Lung Disease 175
Lung Cancer 175
Rotating-Wall Vessel Tumor Models 177
Rotating-Wall Vessel Normal Human Tissue Models as Disease Targets 177
Conclusion 179
References 179
Section 3 Molecular Pathology of Pulmonary and Pleural Neoplasms: General Principles 183
16 Molecular Oncogenesis of Lung Cancer 184
Introduction 184
Oncogene Activation 184
K-ras Activation 185
Erb Family Activation: ErbB1 (EGFR) and ErbB2 (HER2/neu) 185
Myc Activation 185
Other Alterations: Vascular Endothelial Growth Factor, Bcl-2, Myb, Fms, Rlf,Kit/SCR, GRP/GRPR, Raf 186
Alterations of Tumor Suppressor Genes in Lung Cancers 186
The p53 Pathway 186
The Retinoblastoma Pathway: Rb and P16INK4 187
Other Chromosomal Deletions 187
Gene Silencing by MicroRNA 188
Perspectives 188
References 188
17 Genetic Susceptibility 191
Lung Cancer Risk 191
Familial Lung Cancer Risk 191
Lung Cancer Risk in Women and Men 192
Xenobiotic-Metabolizing Enzymes 192
DNA Adducts and Lung Cancer 193
Polymorphisms and DNA Adduct Levels 193
Investigations of Specific Polymorphismsand Susceptibility to Lung Cancer 194
Xenobiotic-Metabolizing Genes 194
Cytochrome P450 Polymorphisms and Lung Cancer Susceptibility 194
CYP2A6 195
Other CYP Alleles 195
Aryl Hydrocarbon Receptor 195
Microsomal Epoxide Hydrolase 195
Glutathione-S-Transferase and Lung Cancer Susceptibility 195
Other Phase II Xenobiotic Enzymes 195
Multiple Xenobiotic-Metabolizing Enzymes 195
DNA Repair Gene Polymorphisms and Lung Cancer Susceptibility 196
Nucleotide Excision Repair Pathway Polymorphisms 196
Other DNA Repair Genes 197
Multiple DNA Repair Genes 197
References 197
18 Prognostic Markers 208
Prognostic Markers 208
Non–Small Cell Lung Cancers 208
c-erbB2 208
Bcl-2 209
p53 209
p63 210
Retinoblastoma Protein 210
Cell Cycle Proteins 210
Epidermal Growth Factor Receptor 210
Murine Double Minute 2 211
ras 211
L-Myc 211
Neuroendocrine Lung Cancers 211
Conclusion 212
References 212
19 Pulmonary Angiogenesis in Neoplasticand Nonneoplastic Disorders 215
Introduction 215
The CXC Chemokines 215
CXCR2 Is the Receptor for Angiogenic ELR+ CXC Chemokine-Mediated Angiogenesis 216
Virally Encoded Chemokine Receptorsand Angiogenesis 217
CXCR3 Is the Major Receptor for CXC Chemokines That Inhibit Angiogenesis 217
Endothelin-1 and Angiogenesis 218
Angiogenesis and Pulmonary Hypertension 218
Angiogenesis and Fibroproliferation in the Lung 219
Chemokines and Angiogenesis in Lung Cancer 220
Non-ELR+ CXC Chemokines Attenuate Angiogenesis Associated with Tumorigenesis 220
Molecular Mechanisms of Angiogenesis 221
The Duffy Antigen Receptor for Chemokines and Tumor Angiogenesis 223
Possible Nonreceptor-Mediated Inhibition of Angiogenesis 223
Conclusion 224
References 224
20 Lung Cancer Stem Cells 228
Stem Cells 228
Cancer Stem Cells 228
Cancer Stem Cell Regulation 229
Clinical Implications of Cancer Stem Cells 230
Lung Cancer Stem Cells 230
References 231
21 Gene Therapy Approaches for Lung Cancer 234
Introduction 234
Mechanism of p53 Tumor Suppression and Rationale for p53 Gene Therapy 234
Preclinical Studies of p53 Gene Replacement 235
Clinical Trials of p53 Gene Replacement 235
Gene Replacement in Combination with Conventional DNA-Damaging Agents in Non–Small Cell Lung Cancer 236
Preclinical Studies 236
Clinical Trials of Tumor Suppressor Gene Replacement Combined with Chemotherapy 236
Clinical Trials of p53 Gene Replacement Combined with Radiation Therapy 236
Systemic Gene Therapy 237
Conclusion 238
References 238
22 Response to Conventional Therapy and Targeted Molecular Therapy 241
Traditional Therapy 241
Predictors of Response to Traditional Therapy 241
Targeted Therapies 242
Epidermal Growth Factor Receptor-Targeted Therapies 242
Monoclonal Antibodies 242
Tyrosine Kinase Inhibitors 242
Antiangiogenesis Therapy 243
Other Potential Targeted Therapies 244
Trastuzumab 244
Pertuzumab 244
Farnesyltransferase Inhibitor Sch66336 244
Retinoids and Rexinoids 244
Antimethylation 244
Small Cell Lung Carcinoma 244
Conclusion 245
References 245
23 Environmental Agents in Lung and Pleural Neoplasms 248
Introduction 248
Mechanisms of Action of Environmental Carcinogens 248
Asbestos: A Unique Carcinogen 249
Properties of Asbestos 249
Asbestos-Associated Lung Cancers 250
Asbestos-Associated Mesothelioma 250
Mechanisms of Asbestos-Induced Carcinogenesis 250
Mechanisms of Asbestos-Induced CellSignaling In Mitogenesis, TumorPromotion, and Progression 250
General Concepts of Mitogen-Activated Protein Kinase Signaling 251
Mitogen-Activated Protein Kinase Signaling, Fos/Jun Proteins, and Activator Protein-1 Activation 251
Asbestos and Mitogen-Activated Protein Kinase Signaling 252
Nuclear Factor-.B Signaling by Asbestos 252
Phosphatidylinositol-3 Kinase/AktSignaling by Asbestos 252
Conclusion 252
References 253
24 Viral Oncogenesis 255
Introduction 255
Mechanisms of Tumorigenesis 256
Cell Proliferation and Carcinogenesis 257
Viruses in Human Tumors 257
Conclusion 260
References 260
Section 4 Molecular Pathology of Pulmonary and Pleural Neoplasms: Specific Histologic Types 263
25 Adenocarcinoma and Its Precursor Lesions 264
Why Is Adenocarcinoma Now the Most Common Lung Carcinoma? 264
Cigarette Smoke, FilteredVersus Unfiltered Cigarettes,and Their Carcinogens 265
The Architecture of Bronchi,Bronchioles, and Alveoli andTheir Cellular Constituents 265
Regeneration and Its Implications 265
Atypical Adenomatous Hyperplasia,Bronchiolar Columnar Cell Dysplasia, Atypical Goblet Cell Hyperplasia, and Other Lesions? 266
The Role of Cancer Stem Cells 266
The Bronchoalveolar Carcinoma Story:Is There Room for a Noninvasive Adenocarcinoma? 267
Genomic Aberrations in Adenocarcinoma 267
Specific Gene Loci in Adenocarcinomas 268
RNA Expression in Adenocarcinoma 271
Proteomics of Adenocarcinoma 273
Regulatory Pathwaysin Adenocarcinoma 274
The Epidermal Growth Factor Receptor System 274
The Platelet-Derived Growth Factor System 275
The Histone Deacetylase System 275
Insulin-Like Growth Factor System 276
The Vascular Endothelial Growth Factor and Angiogenesis System 277
The Nuclear Factor-.B Pathway 277
The Hepatocyte Growth Factor Pathway 278
From Invasion to Metastasis 279
References 279
26 Molecular Pathology of Squamous Cell Carcinoma and Its Precursors 283
Introduction 283
Chromosomal Abnormalities:Loss of Heterozygosity 284
p53 Mutations 285
The p16/Cyclin D1/Cyclin-Dependent Kinase 4/Retinoblastoma Pathway and Aberrant Methylation 286
The PTEN/MMAC1 Tumor Suppressor Gene 286
Telomerase Dysregulation and Upregulation 286
Amplification of Oncogenes 287
Epidermal Growth Factor Receptorand Tyrosine Kinase Inhibitors 287
Autocrine Growth Factors 288
Conclusion 288
References 289
27 Molecular Pathology of Large Cell Carcinoma and Its Precursors 292
Introduction 292
Molecular Studies:Immunohistochemical Markers 294
Lineage Specific Markers 294
Large Cell Carcinoma 294
Large Cell Neuroendocrine Carcinoma 294
Basaloid Carcinoma 294
Lymphoepithelioma-Like Carcinoma 295
Large Cell Carcinoma with Rhabdoid Phenotype 295
Molecular Pathway and Prognostic Markers 295
Large Cell Carcinoma and Large Cell Neuroendocrine Carcinoma 295
Basaloid Carcinoma 295
Studies of Single Genes 299
Large Cell Carcinoma 299
Large Cell Neuroendocrine Carcinoma 300
Lymphoepithelioma-Like Carcinoma 300
Chromosomal Studies and Large Cell Carcinoma 300
Cytogenetic Studies of Large Cell Carcinoma 300
Comparative Genomic Hybridization 300
Large Cell Carcinoma 300
Large Cell Neuroendocrine Carcinoma 300
Loss of Heterozygosity Studies 301
Large Cell Carcinoma 301
Large Cell Neuroendocrine Carcinoma 301
Gene Expression Profiling Studies 301
Proteomics 302
Conclusion 303
References 303
28 Small Cell Carcinoma 306
Introduction 306
Molecular Pathology 306
Signature of Cell Differentiation 306
The Molecular Genetics Alterations Related to Small Cell Lung Carcinoma Pathogenesis: Proliferation and Progression 307
Chromosomal Imbalances 307
The Sonic Hedgehog Pathway 307
Human Achaete-Scute Homolog 1 Expression 307
p53 Pathway Alterations 307
Retinoblastoma Alterations in Lung Cancer 308
Alteration of Upstream Regulators of p53:p14ARF and MDM2 308
E2F1 Overexpression 309
Chromosome 3p Deletion 309
Telomerase Expression 309
Angiogenic Factors 310
Cadherin–Catenin Complex Proteins 310
Tyrosine-Kinase Growth Factor and Receptors 310
References 311
29 Neuroendocrine Carcinomas and Precursors 314
Introduction 314
Histopathologic Defi nitions 314
Molecular Pathology: Differentiation Signs 315
Molecular Alterations Reflecting Malignant Proliferation 315
Carcinoids (Typical and Atypical) 315
Somatic Genetics: Cytogenetics and Comparative Genomic Hybridization 315
p53 Pathway Alterations 315
The Retinoblastoma Pathway 315
Upstream p53 Pathway Alterations 316
The Fas Pathway of Apoptosis 316
Telomerase Inactivation 316
Angiogenic Factors, Growth Factors, and Migration Factors 316
Large Cell Neuroendocrine Carcinoma 316
Somatic Genetics: Cytogenetics and Comparative Genomic Hybridization 316
Molecular Pathology: The p53 and Retinoblastoma Pathways 317
Apoptotic Factors 317
Fas and Fas Ligand 317
Angiogenic Factors 317
Growth Factors and Receptors 317
Adhesion Molecule of E-Cadherin–b-Catenin Complex 317
Diffuse Idiopathic Pulmonary Neuroendocrine Cell Hyperplasia and Tumorlets 318
References 318
30 Pulmonary Lymphomas 320
Introduction 320
Mucosa-Associated Lymphoid Tissue Lymphoma 320
Case 30.1 321
Diffuse Large B-Cell Lymphoma 323
Posttransplantation Lymphoma 323
Pulmonary Lymphoma in Acquired Immunodeficiency Syndrome 323
Case 30.2 324
Lymphomatoid Granulomatosis 325
Conclusion 326
References 326
31 Posttransplantation Lymphoproliferative Disorder 328
Introduction 328
Classification 328
Incidence and Risk Factors 329
Lung Transplantation and Posttransplantation Lymphoproliferative Disorder 329
Pathogenesis 330
Virology of Epstein-Barr Virus 330
In Vitro Epstein-Barr Virus Infection 332
In Vivo Epstein-Barr Virus Infection 333
Persistence of Infection 333
Cellular Signaling Pathway 335
Immunosurveillance and Evasionof the Immune System 336
Restricted Gene Expression During Latent Infection 336
Interference with Cytokines 336
Cytotoxic Activity 336
Patterns of Epstein-Barr Virus Latency and Related Diseases 337
Molecular Histogenesis 338
Genetic Profi le 340
Diagnosis and Evaluation 341
Treatment and Management 342
Prophylaxis 343
Epstein-Barr Viral Load in Immunocompromised Hosts 343
Epstein-Barr Virus–Negative Disease 343
Prognosis 344
References 344
32 Unusual Benign and Malignant Neoplasms of Lung: Molecular Pathology 347
Sclerosing Hemangioma 347
Lymphangioleiomyomatosis 348
Solitary Fibrous Tumor 348
Lipomatous Neoplasms 349
Myxoid Liposarcoma 350
Chondroma and Chondrosarcoma 350
Vascular Lesions 351
Epithelioid Hemangioendothelioma and Angiosarcoma 351
Other Sarcomas 351
Pulmonary Synovial Sarcoma 351
Pulmonary Artery Sarcoma 351
Alveolar Soft Part Sarcoma 352
References 352
33 Primary Versus Metastatic Cancer: Gene Expression Profiling 354
General Comments 354
Background: Value of Immunohistochemistry 354
Molecular Markers in the Differential Diagnosis of Primary Versus Metastatic Tumor to the Lung: Are We There? 355
Molecular Markers in the Differentiation of Synchronous and Metachronous Lung Lesions Versus Recurrence/Metastases 357
References 357
34 Diffuse Malignant Mesothelioma: Genetic Pathways and Mechanisms of Oncogenesis of Asbestos and Other Agents That Cause Mesotheliomas 360
Introduction 360
Mechanisms of Oncogenesis in Mesothelioma 360
Asbestos-Induced Oncogenesis 360
Viruses 361
Radiation 361
Other Etiologic Factors 361
Cytogenetics, Deletion Mapping, and Gene Profiling in Mesothelioma 361
Karyotypic Analysis Studies 361
Comparative Genomic Hybridization Studies 361
Deletion Mapping 362
Gene Profi ling and Mesothelioma 362
Polymorphisms in Genes as Risk Factors for Asbestos-Related Malignant Mesothelioma 363
Tumor Suppressor Gene Inactivation in Mesothelioma 364
Loss of Cyclin-Dependent Kinase Inhibitor Function 364
The p53 Gene 364
The NF2 Gene 365
Tumor Suppressor Gene Methylation in Mesothelioma 365
Simian Virus 40 and Human Mesothelioma 365
Wilms’ Tumor 1 Susceptibility Gene 366
Abnormal Expression of Growth Factors and Cytokines 367
Conclusion 367
References 367
35 Molecular Pathology of Pediatric Tumors of the Lung 371
Introduction 371
Pleuropulmonary Blastoma 371
Immunohistochemistry 372
Cytogenetic and Molecular Studies 372
Relationship of Pleuropulmonary Blastoma to Congenital Cystic Adenomatoid Malformation 372
Inflammatory Myofibroblastic Tumor 374
Cytogenetic and Molecular Studies 374
Prognostic Signifi cance of ALK Expression 375
Etiologic Role of Infectious Agents 375
Malignant Small Round Cell Tumor of the Thoracopulmonary Region 376
Cytogenetic and Molecular Studies in Ewing’s Family of Tumors 376
References 377
Section 5 Molecular Pathology of Pulmonary Infections 380
36 Basis of Susceptibility to Lung Infection 381
Introduction 381
Lung Anatomy and Function 381
Unique Aspects of the Lung Microcirculation 381
Epithelial Cilia and Airway Surface Fluid 382
Cough Reflex 382
Innate Immunity 382
Complement 382
Surfactant 383
Lung Epithelial Cells 383
Alveolar Macrophages 384
Neutrophils 384
Adaptive Immunity 386
T Lymphocytes 387
Natural Killer and Natural Killer T Cells 390
Dendritic Cells 390
Humoral Immunity (B Lymphocytes and Antibodies) 390
Conclusion 391
References 391
37 Molecular Pathology of Viral Respiratory Diseases 394
Introduction 394
General Principles 395
Structure and Invasion 395
Envelope 395
Genome 396
Recombination 396
Viral Pathogenesis 396
Classification 397
Viral Respiratory Diseases 399
Orthomyxoviridae 399
Paramyxoviridae 399
Adenoviruses 401
Coronaviruses 401
Severe Adult Respiratory Distress Syndrome 402
Bunyaviridae (Hantaviruses) 402
Picornaviruses 402
Conclusion 404
References 404
38 Molecular Pathology of Rickettsial Lung Infections 409
Introduction 409
Rickettsial Infections That Impact Lung Structure and Function 409
Rocky Mountain Spotted Fever 410
Clinical Disease and Pathophysiology 410
Early Events in the Rickettsia–Endothelial Cell Interaction 410
Cellular and Tissue Injury 410
Host Innate and Adaptive Immune Responses to Infection 412
Diagnosis 413
Human Monocytic Ehrlichiosis 413
Clinical Disease and Pathophysiology 413
Early Events in the Ehrlichia–Mononuclear Phagocyte Interaction 415
Cellular and Tissue Injury 415
Host Innate and Adaptive Immune Responses to Infection 415
Diagnosis 416
Conclusion 416
References 416
39 Bacteria 419
Introduction 419
Bacterial Causes of Pneumonia 419
Pathogenesis of Pneumonia 419
Pathology 419
Clinical Features 420
Diagnosis 420
Streptococcus pneumoniae 421
Pathogenesis 421
Clinical Features 421
Antimicrobial Resistance 421
Diagnostic Testing 421
Haemophilus influenzae 422
Pathogenesis 422
Clinical Features 422
Antimicrobial Resistance 422
Diagnostic Testing 422
Moraxella catarrhalis 422
Pathogenesis 422
Clinical Features 423
Antimicrobial Resistance 423
Diagnostic Testing 423
Legionella pneumophila 423
Pathogenesis 423
Clinical Features 423
Antimicrobial Resistance 424
Diagnostic Testing 424
Chlamydophila pneumoniae 424
Pathogenesis 424
Clinical Features 424
Antimicrobial Resistance 424
Diagnostic Testing 424
Mycoplasma pneumoniae 425
Pathogenesis 425
Clinical Features 425
Antimicrobial Resistance 425
Diagnostic Testing 425
Bordetella pertussis 426
Pathogenesis 426
Clinical Features 426
Antimicrobial Resistance 426
Diagnostic Testing 426
Staphylococcus aureus 426
Pathogenesis 427
Clinical Features 427
Antimicrobial Resistance 427
Diagnostic Testing 427
Agents with Bioterrorism Potential 427
Pathogenesis 427
Clinical Features 427
Antimicrobial Resistance 428
Diagnostic Testing 428
References 428
40 Immunopathology of Tuberculosis 431
Introduction: Magnitude of Disease 431
Primary and Secondary Tuberculosis Pathology 431
Immune Response to Tuberculosis 434
Conclusion 437
References 437
41 Molecular Pathology of Fungal Lung Infection 441
Introduction 441
Innate Immunity 441
Cellular Component of Immunity 441
Complement Component 442
Adaptive Immunity 442
Cell-Mediated Immunity and Cytokines 442
Dendritic Cells 442
Humoral Immunity 443
Pathology and Pathogenesis of Fungal Infections 443
Aspergillus 443
Coccidioides 444
Histoplasma 444
Molecular Basis of Pathogenesis 444
Pathology 447
Diagnosis 448
Molecular Diagnostic Techniques 449
Serologic Diagnosis 449
Polymerase Chain Reaction 449
Molecular Basis of Therapy 450
Conclusion 450
References 451
42 Parasites 454
Introduction 454
Principles of Parasitic Molecular Pathogenesis 454
Adaptive Immune Response 455
Parasitic Proteases and Their Role in Pathogenesis 456
Molecular Pathogenesis of Pulmonary Protozoan Pathogens 458
Toxoplasmosis 458
Amebiasis 459
Microsporidiosis 459
Cryptosporidiosis 460
Molecular Pathogenesis of Pulmonary Helminthic Pathogens 461
Nematodes 461
Filariasis 461
Strongyloidiasis 461
Trematodes 462
Paragonomiasis 462
Schistosomiasis 463
Cestodes: Echinococcosis 464
Conclusion 464
References 464
Section 6 Molecular Pathology of Other Nonneoplastic Pulmonary Diseases: General Principles 469
43 Inflammation 470
The Inflammatory Response 470
Harmful Effects of Inflammation 471
Innate Immunity: Toll-Like Receptors 471
Acquired Immunity: Macrophages, Dendritic Cells and Antigen Presentation 472
Variants of Inflammation 474
Granulomatous Inflammation 474
Interstitial Inflammation 475
Human Leukocyte Antigen–Linked Lung Disease 476
Conclusion 478
References 478
44 Oxidants and Antioxidants 481
Introduction 481
Oxidants in the Lung 481
Reactive Oxygen Species 481
Reactive Nitrogen Species 482
Antioxidants in the Lung 482
Nonenzymatic Antioxidants 482
Enzymatic Antioxidants 482
Redox-Sensitive Transcription Factors 483
Oxidative Stress-Associated Lung Disease/Injury 484
References 485
45 Epithelial Repair and Regeneration 487
Introduction 487
Steady-State Kinetics of Lung Epithelial Cells 487
Steps in Injury and Repair 487
Formation of A Provisional Matrix 489
Loss of Normal Basement Membrane 489
Functions of the Provisional Matrix 489
Restitution of the Epithelial Barrier 489
Epithelial Cell Dedifferentiation 489
Signals for Dedifferentiation 490
Epithelial Cell Migration 490
Matrix–Epithelial Cell Interactions During Migration 490
Protease Functions in Epithelial Cell Migration 490
Reestablishment of the Normal Basement Membrane 490
Reconstitution of Epithelial Cell Density 491
Epithelial Cell Proliferation 491
Lung Progenitor and Lung Epithelial Stem Cells Roles 491
Bone Marrow Stem Cells in Repair 492
Growth Factor Functions in Epithelial Cell Reconstitution 492
Epithelial Cell Redifferentiation 492
Epithelial Cell Redifferentiation and Transdifferentiation 492
Developmental Signaling Pathways Mediating Differentiation 492
Transcription Factors Mediating Differentiation Following Injury 493
Metaplasia and Compensatory Apoptosis of Epithelial Cell Populations 493
Roles for Growth Factors in Epithelial Cell Repair 493
Epidermal Growth Factor Family 493
Transforming Growth Factor-ß Family 493
Fibroblast Growth Factor 493
Hepatocyte Growth Factor 494
Epithelial Cell Repair Following Prototypic Injuries 494
Airway Epithelial Cell Repair Following Respiratory Virus Infection 494
Morphologic Events Following Respiratory Virus Infection 494
Molecular Correlates of Morphologic Events 494
Mucous Cell Metaplasia Following Respiratory Virus Infection 495
Alveolar Epithelial Cell Repair Following Acute Respiratory Distress Syndrome 495
Establishment of a Provisional Matrix in Acute Respiratory Distress Syndrome 496
Restitution and Reconstitution of the Epithelial Cell Barrier 496
Summary: Epithelial Cell Repair Following Injury 496
References 496
46 Fibrogenesis 501
Introduction 501
Experimental Models of Lung Fibrosis 501
Fibroblastic Foci and the Fibroblast Phenotype 501
Sources of Fibroblasts 503
Mechanisms of Fibrosis 504
Oxidative Stress 504
Apoptosis 504
Transforming Growth Factor-ß 505
Viral Infection 506
Angiogenesis 506
Inherited Forms of Interstitial Lung Disease 507
Surfactant Protein C Mutations 507
Hermansky-Pudlak Syndrome 508
Genetic Studies of Sporadic and Familial Interstitial Lung Disease 508
References 508
47 Stem Cells in Nonneoplastic Lung Disorders 511
Introduction 511
Pulmonary Repopulation by Bone Marrow–Derived Adult Stem Cells 512
Epithelial Cells 512
Endothelial Cells 515
Fibrocytes 515
Resident Pulmonary Stem Cells 516
Large Airways 516
Small Airways 516
Side Population Cells 517
Conclusion 518
References 518
48 Gene Therapy in Nonneoplastic Lung Disease 521
Introduction 521
Gene Therapy in the Lung 521
Administration 521
Barriers to Gene Transfer 521
Cell Entry and Nuclear Entry 522
Physical Methods of Overcoming Gene Transfer Barriers 523
Gene Transfer Efficacy 523
Cystic Fibrosis 524
Stem Cells and Progenitor Cells 525
Cystic Fibrosis Transmembrane Conductance Regulator Protein Function and Safety 525
Vectors 525
Endpoint Assays 527
Future Directions 527
a1-Antitrypsin Deficiency 527
Other Conditions 528
References 528
Section 7 Molecular Pathology of Other Nonneoplastic Pulmonary Diseases: Specific Entities 535
49 Smoking-Related Lung Diseases 536
Effects of Tobacco Smoke on the Respiratory Tract 536
Effects of Toxins 536
Carcinogenic Effects 537
Temperature 537
Other Factors Relevant for the Action of Toxic and Carcinogenic Substances/Particles 538
The Repair Program and Its Impact on the Reaction of the Epithelium Toward Inhaled Toxins 538
The Defence System 538
Mucociliary Escalator and Clearance 538
The Phagocytic System 538
The Enzymes 538
Chronic Obstructive Pulmonary Disease 539
Anatomic Basis 539
Cells and Mediators 540
Epithelial Cells 540
Neutrophils 541
Macrophages 541
Eosinophils 541
Dendritic Cells 541
T Lymphocytes 541
Oxidative Stress 542
Proteases 543
Other Tobacco Smoking-Induced Lung Diseases 543
Pulmonary Histiocytosis X 543
Respiratory Bronchiolitis–Combined Interstitial Lung Disease 544
Combined Respiratory Bronchiolitis–Combined Interstitial Lung Disease and Histiocytosis X 545
Desquamative Interstitial Pneumonia 545
Conclusion 545
References 546
50 Heritable a1-Antitrypsin Deficiency 550
Introduction 550
Heritable a1-Antitrypsin Deficiency 550
Associated Disorders 550
Structural and Cellular Abnormalities 551
A Case For Disease Modifiers 551
Glycoprotein Biosynthetic Quality Control 551
Glycoprotein Structural Maturation 552
Involvement of Asparagine-Linked Oligosaccharides 552
The Current Model 552
Orchestration of Glycoprotein Degradation 554
Precision of Substrate Selection 554
Substrate Recruitment and Proteolysis 554
Potential Therapeutic Approaches 554
References 556
51 Asthma 558
Introduction 558
Molecular Pathogenesis of Asthma 559
Cytokines, Growth Factors, and Related Regulatory DNA 560
Interleukin-4 and Interleukin-13 560
Interleukin-4 Receptor a-Subunit 561
Conserved Noncoding Sequence 1 561
Interleukin-5 and Interleukin-9 561
Transforming Growth Factor-a1 562
Interleukin-1a and Interleukin-1ß 562
Epidermal Growth Factor 563
Vascular Endothelial Growth Factor 563
Endothelin-1 564
Fibroblast Growth Factors, Angiogenin, and Platelet-Derived Growth Factor 564
Tumor Necrosis Factor 564
Interleukin-12 564
Toll-Like Receptors 564
Chemokines and Their Receptors 565
Integrins 565
Transcription Factors 566
Signal Transducer and Activator of Transcription 1 566
Signal Transducer and Activator of Transcription 6 567
GATA3 567
Nuclear Factor-kB 567
T-Box Expressed in T Cells 567
Costimulatory Molecules 567
CD28 and CD134 567
Cytotoxic T-Lymphocyte Antigen 4 568
CD40 568
T-Cell Immunoglobulin and Mucin Domain Protein Molecules 568
Seven Transmembrane Spanning Receptors 568
Complements 3a and 5a 569
Cysteinyl Leukotrienes 569
Prostaglandins 569
Adenosine 570
The ß2-Adrenergic Receptor 570
Muscarinic Acetylcholine Receptors 571
Platelet-Activating Factor 571
Immunoglobulin E and Its Receptors 571
Endogenous and Exogenous Proteinases 571
Matrix Metalloproteinases 572
Trypsin 572
Tryptase 572
Neutrophil Elastase 572
Other Endogenous Proteinases 572
Exogenous Proteinases 572
Miscellaneous Molecules 572
Syndecan-1 572
Gob-5 573
Human Leukocyte Antigens 573
Nitric Oxide Synthase 573
Histamine and Its Receptors 573
Chitinases and Related Molecules 573
Conclusion 574
References 574
52 Cystic Fibrosis 586
Introduction 586
Genetics 586
Structure and Function of the Cystic Fibrosis Transmembrane Conductance Regulator 587
Pathophysiologic Features of Lung Disease in Cystic Fibrosis 588
Diagnosis 589
Clinical Manifestations 589
Function Assays 589
Sweat Test 589
Transepithelial Nasal Potential Difference 589
Treatment Approaches 590
Conclusion 590
References 591
53 Pulmonary Organogenesis and Developmental Abnormalities 593
Lung Organogenesis 593
Introduction 593
Signaling Pathways 594
Wingless Signaling Pathway 594
Sonic Hedgehog 594
Fibroblast Growth Factor 594
Notch 594
Epithelial Growth Factor 594
Transforming Growth Factor-ß/Bone Morphogenic Protein 4 594
Branching 595
Airway 595
Peripheral Airway 595
Alveoli 595
Mesenchyme 595
Vascular Factors 596
Specific Genes and Developmental Abnormalities 596
Conclusion 597
References 597
54 Genetic Abnormalities of Surfactant Metabolism 599
Introduction 599
Overview of Pulmonary Surfactant 599
Respiratory Distress Syndrome 600
Surfactant Protein B 600
Surfactant Protein C 602
Member A3 of the Adenosine Triphosphate Binding Cassette Family of Proteins 604
Lung Pathology Associatedwith Inborn Errors of Surfactant Metabolism 604
Genetic Testing 608
Other Proteins Important in Surfactant Metabolism Linked to Genetic Diseases 609
Pulmonary Alveolar Proteinosis 609
Conclusion 609
References 610
55 Usual Interstitial Pneumonia 616
Introduction 616
Pathogenesis 616
DNA Microarray Studies 617
Molecular Pathways Involved in Alveolar Damage and Reepithelialization 617
Molecular Characterization of Fibroblast Foci 619
Molecular Pathways Involved in Bronchiolar Reepithelialization 620
Molecular Characterization of Epithelial Cells in Fibroblast Foci 621
References 622
56 Sarcoidosis: Are There Sarcoidosis Genes? 625
Introduction 625
Morphology and Its Implications 625
Variants of Sarcoidosis 625
Löfgren’s Disease/Acute Sarcoidosis 625
Nodular Sarcoidosis 625
Necrotizing Sarcoid Granulomatosis 626
What Is the Meaning of Indistinguishable Differentials? 626
The Cells in Sarcoidosis 627
T Lymphocytes 627
Epithelioid Cells 627
Giant Cells (Foreign Body and Langerhans Type) 628
Mycobacteria and Other Trigger Mechanisms—Is Sarcoidosis an Infectious Disease? 628
Risk Factors 628
The Steps of an Immune Reaction and What Might Happen in Sarcoidosis 629
Antigen Uptake and Processing 629
Antigen Presentation, Costimulatory Molecules, and Gene Polymorphisms and Where They Come Into Play 630
Human Leukocyte Antigen Class I Genes 630
Human Leukocyte Antigen Class II Genes 630
Effector Mechanisms, the Lymphocyte–Macrophage Network, and Gene Expression in Sarcoidosis 631
Disease Modifier Genes and Aspects of Organ Involvement in Sarcoidosis 632
References 633
57 Histiocytic Diseases of the Lung 636
Introduction 636
Pulmonary Histiocytosis X 636
Clinical Disease 636
Pathologic Features 636
Cellular and Molecular Biology 636
Erdheim-Chester Disease 637
Clinical Disease 637
Pathologic Features 637
Cellular and Molecular Biology 637
Lysosomal Storage Disorders 638
Gaucher’s Disease 638
Clinical Disease 638
Pathologic Disease 638
Cellular and Molecular Biology 638
Niemann-Pick Disease 638
Clinical Disease 638
Pathologic Disease 638
Cellular and Molecular Disease 638
Hermansky-Pudlak Syndrome 639
Clinical Disease 639
Pathologic Disease 639
Cellular and Molecular Biology 640
References 640
58 Pulmonary Arterial Hypertension 643
Introduction 643
Pathology 643
Genetics 646
Bone Morphogenetic Protein Receptor Gene Mutations 646
Serotonin Transporter Gene Overexpression 647
Pathogenesis 647
Role of Bone Morphogenic Protein and Its Receptor 647
Role of Serotonin and Serotonin Transporters 649
Role of the Endothelium 649
Extracellular Matrix Remodeling 650
The Thrombotic System 650
Inflammatory Mechanisms 650
Conclusion 651
References 651
59 Immunopathology of Pulmonary Vasculitides 653
Introduction 653
Pathologic Features 654
Molecular Pathology 656
Antineutrophil CytoplasmicAntibody–Associated Vasculitides 657
T Cells in Antineutrophil Cytoplasmic Antibody–Mediated Vasculitis 657
Leukocyte–Endothelial Cell Interaction 658
Cytokines in Vasculitides 658
Transforming Growth Factor-ß 659
Other Cytokines 659
Interferon-a 659
Chemokines 660
Adhesion Molecules 660
Apoptosis in Wegener’s Granulomatosis 660
References 661
60 Asbestosis and Silicosis 667
Introduction 667
Asbestosis 667
Silicosis 669
Conclusion 669
References 669
Index 672

"Section 5 Molecular Pathology of Pulmonary Infections (p. 369-370)

36 Basis of Susceptibility to Lung Infection

Frank C. Schmalstieg and Armond S. Goldman

Introduction

The myriad microbial pathogens encountered by the lung presents a daunting challenge to the human immune system. Nowhere else in the body is such a vast surface area (approximately 100 m2)1 directly exposed to airborne pathogens at about 20 times per minute. Not only is the area and exposure extreme, but the underlying blood circulation is only two cell layers, of about 0.5 μm each, removed from the alveolar surface. Furthermore, gravity and manifold branching of bronchioles and bronchi interfere with the expulsion of these organisms and tissue debris that occurs during lung infection. It is not surprising, then, that pneumonias are among the most common infectious diseases in the United States.

Understanding the susceptibility to lung infection requires a comprehension of (1) the anatomy and function of the lung, (2) environmental exposures, (3) systemic and mucosal immune functions, (4) virulence of pathogens, and (5) genetic variabilities of the host defenses. Numerous “experiments of nature” and identi- ? cation of the molecular mechanisms of pathogen entry into lung cells especially have provided unique insights into understanding immune aspects of host susceptibility. More recently, rapid, high volume methods of analyzing potential genetic determinants for host susceptibility to speci? c pathogens have shown considerable promise. These considerations and their results are explored in some detail in this chapter.

Lung Anatomy and Function

Unique Aspects of the Lung Microcirculation

Three distinct circulations supply the lung and airways with blood. They are the tracheal, bronchial, and pulmonary circulations. The tracheal arteries branch from the superior and inferior thyroid arteries and drain to the inferior thyroid venous plexus. More importantly, the bronchial arterial supply is from the thoracic aorta, and the venous drainage from this artery is largely (∼70%) anastomosed to the pulmonary circulation in a precapillary location3 in the sheep. This also likely occurs in humans.

These anastomoses are signi? cant because neutrophils may be in? uenced by mediators from airway epithelium and then interact directly with the pulmonary capillaries, thus providing a connection with in? ammation in the airway and in the alveolar capillaries. In this regard, the capillary diameter in the bronchial microcirculation is about 8.5 μm but only approximately 5.5 μm in the pulmonary capillaries.4 Neutrophils have to deform during passage through the pulmonary capillaries (Figure 36.1) because of their relatively large diameter (10– 15 μm).

In contrast, erythrocytes pass through those capillaries more readily because of their smaller diameters. Delay in the passage of neutrophils results in a relative increase in neutrophil concentration in the pulmonary capillaries.5 This may be an adaptive modi? cation for better control of any organisms breaching the extensive and exposed surfaces of the alveoli.

The slowing and momentary stopping of neutrophils in the pulmonary capillaries under certain stimuli may allow selectin- and integrin-independent migration of these cells from the capillaries.6,7 The bronchial circulation is also unique in that airway injury can stimulate a ? vefold increase in bronchial blood ? ow in sheep.

Although the increased blood ? ow during injury amounts to less than 3% of the cardiac output, neutrophils activated in the bronchial microcirculation may be directly delivered to the pulmonary capillaries to produce damage. In fact, bronchial artery ligation decreases lung edema in a sheep model of smoke and burn injury.9 The anatomy of the lung then potentially allows damage in the airway to produce in? ammatory changes in the lung that may enhance lung protection or lead to further damage under some circumstances."