Introduction to Antibody Engineering 3030546292, 9783030546298

Table of contents :
Preface
Contents
1: Introduction by the Editors
2: Antibodies: A History of Their Discovery and Properties
What You Will Learn in This Chapter
2.1 Introduction
2.2 Early Beginnings
2.3 Serum as the Protection Matrix
2.4 Specificity and the Nature of Proteins
2.5 Theories of Protein Structure
2.6 Antibody Sequences: Homogeneous or Heterogeneous?
2.7 γ-Globulin: Isotypes and Allotypes
2.8 The Structural Basis of Antibody Recognition Revealed
2.9 The Origins of Antibody Diversity
2.10 The Fc Region and Effector Functions
2.11 The Modern Era
2.12 The Antibody Engineering Revolution
References
3: Monoclonal AntibodiesMonoclonal antibodies (mAbs) and HybridomasHybridomas
What You Will Learn in This Chapter
3.1 The First Monoclonal Antibodies
3.2 Sequence, Structure and Function of Antibodies
3.2.1 Overall Structure
3.2.2 Variable Domains
3.2.3 Constant Domains
3.3 The Hybridoma Method
3.3.1 The Starting Point: Antibody-Producing B-Cells
3.3.2 ImmunizationImmunizations
3.3.3 Myeloma Cell Lines Suitable for Fusion
3.3.4 Cell FusionCell fusion
3.3.5 Identification of Individual Hybridoma Clones
3.3.6 Monoclonality
3.4 From Mouse to Human Monoclonal Antibodies
3.4.1 Chimeric Antibodies
3.4.2 Nomenclature of Monoclonal Antibodies
3.4.3 Humanized Antibodies
3.4.4 Fully Human Monoclonal Antibodies
3.5 Antibody Fragments
Questions
Take Home Message
References
4: Antibody Display Systems
What You Will Learn in This Chapter
4.1 Introduction
4.2 Phage DisplayPhage display
4.3 YeastYeast Surface Display
4.4 Mammalian DisplayMammalian display
4.5 E. coli DisplayE. coli display
4.6 Ribosome Display
4.7 cDNA DisplaycDNA display
4.8 B-Cell Cloning
Take Home Message
References
5: Transgenic AnimalsTransgenic animals for the Generation of Human Antibodies
What You Will Learn in This Chapter
5.1 The Concept of Using Transgenic Animals to Generate Human Therapeutic Antibodies
5.2 Strategies in Developing Transgenic Platforms for Human Antibody Discovery
5.2.1 Transgenic Strategies
5.2.2 Animals with Knockout of Endogenous Ig Production
5.2.3 Human IgH Gene Loci in Transgenic Constructs
5.2.4 Human Igĸ and Igλ Gene Loci in Transgenic Constructs
5.3 Examples of Currently Available Transgenic Platforms for Human Antibody Discovery
5.3.1 HuMAb-MouseHuMab-Mouse and XenoMouse
5.3.2 Tc Mouse, Tc Bovine and Tc Goat (Caprine)
5.3.3 OmniRat, OmniMouseOmniMouse and OmniChicken
5.3.4 VelociMouseVelociMouse, Kymouse and Trianni Mouse
5.3.5 Transgenic Platforms Expressing Different Formats of Antibodies
5.3.5.1 OmniFlicOmniFlicand OmniClicOmniClic
5.3.5.2 HCAb Transgenic Mice (Harbour Biomed), Humabody VH Platform and UniRat
5.4 Strategies in Antibody Discovery from Transgenic Platforms
Take Home Messages
Further Reading
References
6: Applications of Antibodies in Therapy, Diagnosis, and Science
What You Will Learn in This Chapter
6.1 Application of Antibodies in Therapy
6.1.1 Cetuximab
6.1.2 Trastuzumab
6.1.3 Rituximab
6.1.4 Ipilimumab
6.1.5 Nivolumab
6.1.6 PembrolizumabPembrolizumab (Keytruda)
6.1.7 Avelumab
6.1.8 Adalimumab
6.1.9 BlinatumomabBlinatumomab (Blincyto)
6.1.10 Emicizumab
6.2 Applications of Antibodies in Diagnosis
6.3 Application of Antibodies in Science
6.3.1 Immunoprecipitation
6.3.2 Chromatin ImmunoprecipitationChromatin immunoprecipitation (ChIP)
6.3.3 Western Blotting
6.3.4 Enzyme-Linked Immunosorbent Assay (ELISAEnzyme-linked immunosorbent assay (ELISA))
6.3.5 ImmunohistochemistryImmunohistochemistry (IHC)/ImmunocytochemistryImmunocytochemistry (ICC)
6.3.6 Immuno-PCR and Proximity Ligation Assay
6.3.7 Flow CytometryFlow cytometry
6.3.8 Mass SpectrometryMass spectrometry (MS)
Take Home Message
References
Further Reading
7: Bispecific Antibodies
What You Will Learn in This Chapter
7.1 Introduction
Questions
7.2 History of Bispecific Antibodies
Questions
7.3 Mode of Action of Bispecific Antibodies Today
7.3.1 BsAbs for Bridging Different Cell Types
7.3.2 Signaling Inhibition by Bridging Receptor Molecules
7.3.3 Overcoming Ligand Redundancy
7.3.4 Targeting Two Epitopes of the Same Antigen: Biparatopic bsAbs
7.3.5 Enzyme Mimetics
7.3.6 BsAbs Enabling Transport: Piggyback Molecules
Questions
7.4 Formats of Bispecific Antibodies
7.4.1 Fragment-Based Bispecific Antibodies
7.4.2 Symmetric Ab Formats
7.4.3 Asymmetric bsAb Formats
Questions
7.5 Outlook for Bispecific Antibodies
7.6 Conclusion
Take Home Messages
References
8: Antibody-Drug Conjugates
What You Will Learn in This Chapter
8.1 Introduction to ADCs
8.2 Milestones of ADC Development
8.3 Targets and Antibodies Utilized for ADCsAntibody-drug conjugates (ADCs)
8.4 Cytotoxic ADC Payloads
8.5 ADC Linkers
8.6 Conjugation Technologies for ADC Generation
Take Home Messages
References
9: Alternative Binding Scaffolds: Multipurpose Binders for Applications in Basic Research and Therapy
What You Will Learn in This Chapter
9.1 What Are Alternative Binding Scaffolds, What Are Their Features, and What Is Their Potential?
9.2 Details on the Most Advanced Alternative Binding Scaffolds
9.2.1 Tenth Type III Domain of Fibronectin (Monobodies, Adnectins)
9.2.2 Affibodies
9.2.3 Affitins/Nanofitins
9.2.4 Avimers
9.2.5 Cysteine-Knot Miniproteins (Knottins)
9.2.6 Designed Ankyrin Repeat Proteins
9.2.7 Fynomers
9.2.8 Kunitz Domain Inhibitors
9.2.9 Lipocalins (Anticalins)
9.3 Alternative Binding Scaffolds in the Clinic
9.4 Alternative Binding Scaffolds as Tools in Basic Research and Beyond
9.5 Future Directions
Take Home Messages
References
10: Chimeric Antigen Receptor (CAR) Redirected T Cells
What You Will Learn in This Chapter
10.1 The Prototype Chimeric Antigen Receptor (CAR, T-Body, Immunoreceptor)
10.2 Modular Composition of a CAR: The Extracellular CAR Domains
10.2.1 The Binding Domain
10.2.2 The Spacer Domain
10.2.3 The Transmembrane Region
10.2.4 Intracellular Signaling Domains
10.3 TRUCK: The ``Fourth Generation´´ CAR T Cell
10.4 CAR T Cells with Dual Specificities, Combinatorial Antigen Recognition, and Conditional CARs
10.5 Universal CARs with Engrafted Multiple Antigen Specificities
10.6 Switch CARs Convert a Suppressor into an Activation Signal
10.7 Inhibitory CARs: iCARs
10.8 Allogeneic CAR T Cells and CAR NK Cells
10.9 Manufacturing CAR T Cells for Clinical Applications
10.10 Adoptive Therapy with CAR T Cells Induces Lasting Remissions in Hematologic Malignancies
10.11 The Challenges of CAR T Cells in Treating Solid Cancer
10.12 CAR T Cell Therapy Is Associated with Toxicities
10.12.1 Systemic Toxicities
10.12.2 ``On-Target Off-Tumor´´ Toxicities
10.12.3 ``Off-target Off-tumor´´ Toxicities
10.12.4 Strategies to Ameliorate CRS
10.13 Challenges in CAR T Cell Therapy
10.13.1 Which Is the Best Tumor-Selective Antigen Suitable for Targeting?
10.13.2 How to Optimize the CAR Architecture?
10.13.3 How to Establish Long-Term Cancer Control After CAR T Cell Therapy?
10.13.4 Which T Cell Subset Provides Long-Term Tumor Control?
10.13.5 How Can CAR T Cell Manufacturing Be Adapted to an Increasing Number of Patients?
10.13.6 How to Balance CAR T Cell Efficacy and Side Effects?
10.13.7 Do We Need Specific Pre-conditioning for Each Cancer Type?
10.13.8 How to Activate the Immune Network to Induce a Broad Inflammatory Antitumor Response?
10.14 CAR T Cells for the Treatment of Other Diseases
Take Home Messages
References
11: Improvement of Key Characteristics of Antibodies
What You Will Learn in This Chapter
11.1 Improving the Natural Functions of Antibodies to Create Therapeutics
11.2 Antigen Binding
11.2.1 Binding Epitope and Affinity
11.2.2 Creating a Therapeutic Antibody with pH Sensitivity or `pH Switch´
11.3 Improving and Optimising the Interactions with Fc Receptors
11.4 Complement Activation and Inactivation
11.5 Improving Serum Half-Life to Decrease Dosing Frequency
11.6 Immunogenicity of Therapeutic Antibodies
11.7 Antibody Fragments
11.8 Improving Biophysical Properties of Therapeutic Antibodies
11.8.1 Aggregation
11.8.2 Thermal Denaturation
11.8.3 Fragmentation, Deamidation and Oxidation
11.8.4 Computational Design Tools
Take Home Messages
References
12: Engineering Therapeutic Antibodies for Development
What You Will Learn from This Chapter
12.1 Introduction
12.2 Safety Considerations
12.3 Examples of Target-Dependent Side Effects of mAbs
12.4 Immunogenicity of Biotherapeutics
12.5 What Causes Immunogenicity?
12.6 Mechanisms Leading to an ADA Response
12.6.1 T Cell-Dependent Immune Response
12.7 T Cell-Independent Immune Response
12.8 Clinical Consequences of Immunogenicity
12.9 Engineering mAbs for Safety and Minimal Immunogenicity
12.10 Humanization
12.11 Selection of Isotypes
12.12 Heterogeneity of Therapeutic mAbs
12.13 Quality Attributes of mAbs Can Impact Safety and Efficacy
12.14 Protein Engineering to Control mAb Variants
12.15 Improved Manufacturability to Control mAb Variants
12.16 mAb Industrial Manufacturing
12.17 Considerations for Intended Use and mAb Formulation into Drug Product
12.18 Formulation Development
12.19 Closing Remarks
Take Home Messages
References
13: Eukaryotic Expression Systems for Upstream Processing of Monoclonal Antibodies
What You Will Learn in This Chapter
13.1 Introduction
13.1.1 Antibodies and Different Antibody Formats
13.1.2 Product Quality Attributes
13.1.2.1 Glycosylation
13.1.2.2 Charge Distribution
13.1.2.3 Molecular Size
13.1.2.4 Oxidation
13.1.2.5 Structure
13.2 Antibody Production in Mammalian Cells
13.2.1 Host Cell Lines
13.2.2 Cell Culture Medium
13.2.3 Environmental Cultivation Parameters
13.2.4 Mode of Bioreactor Operation
13.3 Antibody Production in Yeast and Filamentous Fungi
13.3.1 General Characteristics of the Expression Systems
13.3.2 Glycosylation and Glycoengineered Production Strains
13.3.3 Antibody Production in Yeast
13.3.4 Antibody Production in Filamentous Fungi
13.4 Conclusion
Take Home Messages
References
14: Antibody Validation
What You Will Learn in This Chapter
14.1 Introduction
14.1.1 State of the Art and Problem Setting
Questions
14.1.2 Advantages of Polyclonal Antibodies
Questions
14.2 Cornerstones for Antibody Validation for Different Scientific Applications
14.2.1 Standards for Reporting the Use of Antibodies in Scientific Publications
Questions
14.2.2 Publicly Available Antibody Databases
Questions
14.2.3 Minimum Information About a Protein Affinity Reagent Proposal
Questions
14.3 Scientific Incentives for Antibody Validation
Questions
14.4 The Human Protein Atlas
14.4.1 Introduction to the Human Protein Atlas
14.4.2 History of Human Protein Atlas
14.4.3 Standard Antibody Validation
14.4.4 Enhanced Antibody Validation
Questions
14.5 Start-off Simple: 10 Validation Rules for Diagnostic and Analytical Antibodies
Questions
14.6 Conclusion
Take Home Messages
References
Index