Handbook of Glycomics (eBook)

Front Cover 1
Handbook of Glycomics 4
Copyright Page 5
Contents 6
List of Contributors 8
Preface 12
Acknowledgments 16
Section I: Glycoconjugate Structural Analysis 18
Chapter 1. High-Sensitivity Analytical Approaches to the Analysis of N-Glycans 20
Introduction 20
Release of N-Glycans from Glycoproteins 21
Purification of N-Glycans 23
Analysis of Glycan Mixtures 26
Conclusions 54
References 55
Chapter 2. O-Glycan Complexity and Analysis 62
Introduction 62
O-Glycan Complexity 63
Analysis of Released O-Glycans 66
Analysis of O-Glycopeptides 70
Conclusions 70
References 71
Chapter 3. Glycosaminoglycans 76
Introduction 76
Isolation of GAGs 78
Purification of Individual GAGs 80
Structure Analysis 81
Conclusion 90
References 91
Section II: Glycotranscriptomics 98
Chapter 4. Isotopic Labeling of Glycans for Quantitative Glycomics 100
Introduction 100
Overall Strategy of Isotope Labeling of Glycans for Quantitative Glycomics 101
Isotope-Coded Reagents for Glycan Analyses and Analytical Approaches 103
Concluding Remarks 108
References 109
Chapter 5. Glycotranscriptomics 112
Introduction 112
Overview of Glycan Biosynthesis in Animal Systems 114
Identification of Genes Involved in Glycan Biosynthesis 121
Overview of Transcript Analysis and Gene Expression Methods 125
Analysis of Gene Expression Data 134
Examples of Correlation of Transcript Analysis Data with Protein and Structural Data 135
Future Directions 137
References 138
Section III: Protein–Glycan Interactions 154
Chapter 6. Glycan-Binding Proteins and Glycan Microarrays 156
Introduction 156
Construction of Glycan Microarrays 157
Overall Strategy of Glycan Arrays: the Big Picture 162
Methods for Detecting Binding of GBPs to Glycan Arrays 163
Collection and Presentation of Data from a Large Glycan Microarray 167
Use of Glycan Arrays to Investigate Specificity of Glycan-Binding Proteins 168
Virus Binding to Glycan Arrays 171
Limitations of Glycan Arrays 173
Concluding Remarks 174
References 174
Chapter 7. Chromatographic and Mass Spectrometric Techniques 178
Current Status of Understanding about Glycans 178
Basic Approaches to Structural Glycomics 178
The Use of Lectins in Structural Glycomics 181
Methods for Interaction Analysis of Lectins and Glycans: A Basis of Lectin Study 182
Concluding Remarks 189
References 189
Section IV: Glycobioinformatics 194
Chapter 8. Integration of Glycomics Knowledge and Data 196
Background and Motivation 196
Bioinformatic Approaches to Glycobiology 199
Conclusions 211
References 212
Chapter 9. KEGG GLYCAN for Integrated Analysis of Pathways, Genes, and Glycan Structures 214
Introduction 214
Glycan Biosynthesis and Metabolism 215
Genes Related to Glycan Biosynthesis 217
Glycan Structures 220
Bioinformatics Approach to Glycomics Research 221
Algorithms for Feature Extraction of Glycan Structures 223
Concluding Remarks 225
References 226
Chapter 10. Carbohydrate Structure Databases 228
Introduction 228
Current Established Carbohydrate Structure Databases 230
New Database Initiatives 234
Case Studies 239
Conclusion and Outlook 244
References 247
Section V: Glycomes 252
Chapter 11. Glycomics of the Immune System 254
Glycosylation in the Immune System 254
Mammalian Lectins of the Immune System 255
Current Approaches in the Study of Immune Cell Glycomes 256
Cellular Glycomes of the Innate Immune System 259
Cellular Glycomes of the Adaptive Immune System 265
Conclusions 274
References 274
Chapter 12. Mouse and Human Glycomes 280
Introduction 280
Mouse Glycomics 283
Human Glycomics 308
Glycome Comparisons 335
Data Repositories 339
Current Limitations and the Future 340
References 341
Chapter 13. Genetic and Structural Analysis of the Glycoprotein and Glycolipid Glycans of Drosophila melanogaster 346
Introduction, Overview, and Scope 346
N-Linked Glycoprotein Glycans 347
O-Linked Glycoprotein Glycans 351
Glycosphingolipid Glycans 353
Summary and Perspective 356
References 357
Chapter 14. Malaria 364
Introduction 364
Life Cycle 365
Glycobiology of P. falciparum 366
Experimental Results 366
Direct Glycosylation by the Parasite 373
Conclusion 374
Overall Summary 375
References 376
Chapter 15. Glycomics in Unraveling Glycan-Driven Immune Responses by Parasitic Helminths 384
Introduction 384
Glycan Structures in Helminths 385
Recognition of Parasite Glycans by Collectins of the Innate Immune System 397
Parasite Glycans are Key Players in Helminth-Induced Immune Regulation 397
Secretion of Lectins by Parasitic Helminths 400
Anti-Glycan Humoral Responses 401
Diagnostic Approaches Employing Helminth Glycans 402
Conclusions and Future Prospects 402
References 403
Section VI: Disease Glycomes 414
Chapter 16. Cancer Glycomics 416
Introduction 416
Analysis of Glycans on Specific Glycoproteins 420
Comparative Glycoproteomics of Serum to Identify Potential Tumor Markers 421
Glycans Released from Serum Glycoproteins 424
Use of Targeted Glycoproteomics to Identify Changes in Glycoprotein Expression in Cancer Serum 427
Comparison of O-Linked Glycans in Cancer Serum and on Cancer Cells 429
Comparative Glycoproteomic Analysis of Cancer Cells and Tissues 431
Antibody Arrays to Detect Glycan Variation on Glycoprotein Markers 434
Antibodies to Glycan Epitopes Expressed in Cancer Tissues 435
Conclusion 435
References 437
Chapter 17. Introduction to Human Glycosylation Disorders 448
Introduction 448
Brief History and Nomenclature 448
Glycobiologists, Clinicians, and Geneticists Collaborate in Patient Diagnosis 451
Spectrum of Disorders 452
N-Glycan Defects 452
Animal Models of N-Glycosylation Disorders 455
Congenital Muscular Dystrophies 458
Defects in Glycosphingolipid and Glycosylphosphaditylinositol Biosynthesis 462
Defects in O-GalNAc Glycan Biosynthesis 463
Defects in O-Fucose-Linked Glycans 463
Defects in Glycosaminoglycan Synthesis 464
Opportunities 466
Possible Therapies for CDG-Ia? 467
Some Unanswered Questions 468
Conclusions 469
References 470
Index 482
A 482
B 482
C 482
D 483
E 484
F 484
G 484
H 486
I 487
K 487
L 487
M 488
N 489
O 489
P 489
Q 489
R 489
S 489
T 490
U 490
W 490
Z 490
Color Plates 492