System Vaccinology: The History, the Translational Challenges and the Future

438 Pages·2022·44.487 MB·English

by  Vijay Kumar Prajapati

System Vaccinology

System Vaccinology
The History, the Translational Challenges
and the Future
Edited by
Vijay Kumar Prajapati
Department of Biochemistry, School of Life Sciences,
Central University of Rajasthan, Ajmer, Rajasthan, India
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Contents
Contributors xiii
Part I
History and introduction
1. History of vaccine: from centuries to present
Rupal Ojha, Vijay Kumar Prajapati
1.1 Introduction 3
1.2 Generations of vaccines 5
1.2.1 First-generation vaccines 5
1.2.2 Second-generation vaccines 7
1.2.3 Third-generation vaccines 8
1.3 The present scenario in the field of vaccine development 10
1.4 Conclusion 12
References 12
2. Evolution and development of vaccines against major
human infections 17
Utkarsha Sahu, Prashant Khare
2.1 Introduction 17
2.2 Vaccines against major human infections 19
2.2.1 Bacterial disease vaccines 19
2.2.2 Viral disease vaccines 21
2.2.3 Protozoan disease vaccines 22
2.3 Discussion 24
References 25
Part II
Immunology of vaccine designing
3. Vaccine Omics: role of bioinformatics in vaccinology
Shivani Krishna Kapuganti, Aparna Bhardwaj, Namyashree Nayak,
Taniya Bhardwaj, Prateek Kumar, Rajanish Giri
3.1 History of vaccinology 33
3.2 Immune response involved in vaccination 34
vv
vi Contents
3.3 Vaccine immunoinformatics and in-silico designing of vaccines 38
3.4 Commonly used epitope predictors 43
3.4.1 Prediction of B-cell epitopes 43
3.4.2 Prediction of T-cell epitopes 45
3.5 Bioinformatic tools for analysis of the vaccine construct 47
3.5.1 Prediction of antigenicity 47
3.5.2 Prediction of allergenicity 47
3.5.3 Analysis of toxicity, solubility, and physicochemical
properties 48
3.6 Structure modeling of the vaccine construct 49
3.7 Disorder perspective in vaccine construction 49
3.8 Future perspectives 50
Acknowledgments 50
Conflict of Interest 50
References 51
4. Vaccine engineering & structural vaccinology
Fabiana A Carneiro, Juliana dos Reis Cortines, Victor Alejandro Essus,
Isis Botelho N da Silva
4.1 Introduction 55
4.2 Methodology used for vaccine production 57
4.2.1 Attenuated and inactivated microorganisms 57
4.2.2 Vectors 58
4.2.3 Protein conjugate vaccine 59
4.3 Reverse vaccinology 60
4.4 Structural vaccinology 61
4.4.1 Multiepitope peptide vaccines 62
4.5 Vaccine engineering 64
4.5.1 Vaccines based on virus-like particles 65
4.5.2 Engineering adjuvants 70
4.6 Immunogenicity 72
4.6.1 Biomolecular origin of antigens and the induced immune
response 72
4.6.2 Vaccine administration site and immune response
determination 80
4.7 Challenges in mass vaccination 81
References 82
5. Infection, immunity, and vaccine development
Bhawana Singh, Awnish Kumar, Rahul Tiwari, Shashi Bhushan Chauhan,
Om Prakash Singh, Santosh K Singh, Vibhav Gautam, Shyam Sundar,
Rajiv Kumar
5.1 Introduction 87
5.2 Basic concept of vaccine immunology 88
5.2.1 Innate immunity 89
5.2.2 Adaptive immunity 91
Contents vii
5.3 Immunological memory 94
5.3.1 T-cells memory 95
5.3.2 B-cells memory 97
5.4 Vaccine development 99
5.5 Concluding remarks 103
Acknowledgments 104
References 104
Further reading 109
6. Immune responses to vaccines: from classical to
systems approaches
João Lucas Lima Calandrini de Azevedo, Viviane Schuch, João Marcos
Maia Silva, André Guilherme Costa Martins, Luiz Gustavo Gardinassi,
Helder I Nakaya, Simone Gonçalves Fonseca
6.1 Introduction 111
6.2 Immune response to vaccines 113
6.2.1 Innate immune response 114
6.2.2 Adaptive immune response 117
6.2.3 Humoral immune response 118
6.3 Approaches for assessing the immune response following
the vaccination 122
6.3.1 Neutralizing antibody assay 122
6.3.2 Effector functions of antibodies 124
6.3.3 Enzyme-linked immunosorbent assay 125
6.3.4 Enzyme-linked immunospot (ELISPOT) 125
6.3.5 Cytokine multiplex 126
6.3.6 Multiparametric flow cytometry—cell phenotype and
cytokine production 127
6.3.7 Time-of-flight mass cytometry—CyTOF 129
6.4 Other factors that influence the immune response to a vaccine 129
6.5 Systems vaccinology 130
6.5.1 Transcriptomics 131
6.5.2 Proteomics 134
6.5.3 Metabolomics 135
6.5.4 Data integration 136
6.5.5 Network analysis in vaccinology 138
6.6 Concluding remarks 140
Acknowledgments 140
References 140
7. Leptin: an immunological adjuvant to improve vaccine
response in infectious diseases
Radheshyam Maurya, Madhulika Namdeo
7.1 Introduction 153
7.2 Fundamentals of leptin 154
7.3 Leptin receptor and leptin signaling 155
7.4 Leptin signaling in immune cells 157
7.5 Leptin and innate immunity 157
viii Contents
7.6 Leptin in adoptive immunity 159
7.7 Leptin deficiency and infection diseases 160
7.8 Leptin as an immunological adjuvant 165
References 168
8. Polymer-based adjuvant requirements for vaccines
Edna Soares, Olga Borges
8.1 Introduction 177
8.2 Vaccine design for viral infections 179
8.3 Mimicking pathogens 180
8.4 The case of DNA vaccines 181
8.5 The importance of new adjuvant development 181
8.6 Adjuvant particulate form 184
8.7 Pathogen-associated molecular patterns (PAMPs) as
immunopotentiators 185
8.8 The case of oral administration of vaccines 186
8.9 Polymer-based particulate adjuvants in oral vaccine formulation 188
8.10 Biodegradable polymer-based particles 190
8.11 Natural occurring polymers—polysaccharides 192
8.11.1 Chitosan 193
8.11.2 β-glucans 194
8.12 Summary 197
References 198
Part III
Assessment of vaccine efficacy and its delivery
9. Circadian rhythmicity and vaccination
María Maximina Bertha Moreno-Altamirano, Jacqueline Oliva-Ramírez,
Francisco Javier Sánchez-García
9.1 Circadian cycles 207
9.2 Circadian clock 210
9.3 Circadian rhythmicity and immunity 211
9.4 Circadian rhythmicity and infection 214
9.5 Aging, immunosenescence, and circadian rhythmicity 217
9.6 Time of the day immunization/vaccination and immune response 218
9.7 Challenges, outstanding questions, and future directions 220
Acknowledgments 221
References 222
10. Controlled human infection modeling and vaccine
development
Adrian Wildfire
10.1 Introduction 231
10.2 The history of human challenge 233
Contents ix
10.3 Principles of human challenge 235
10.4 Applications and limitations 237
10.5 Challenge agents—selection and manufacture 240
10.6 Characterization trials 243
10.7 Clinical aspects of performing human challenge trials 245
10.7.1 Trial population/cohort 245
10.7.2 Eligibility criteria and adverse events 246
10.7.3 Ethical considerations and study restrictions 247
10.8 Regulatory considerations 248
10.9 Summary 252
References 253
11. Preclinical testing of vaccine candidates in animal models
Katharine C. Carter, Derya T. Ata, Raphael T. Aruleba, Ramona Hurdayal
11.1 Introduction 257
11.2 Types of animal models used in vaccine studies 260
11.2.1 Small and large animal models 260
11.2.2 Natural, surrogate, surgical, and experimental models 262
11.2.3 Humanized mice 262
11.3 Immunity to vaccines 264
11.3.1 CD4+ T cell activation 264
11.3.2 CD8+ T cell activation 265
11.3.3 B-cell activation 265
11.4 Predictors of vaccine-induced protective immunity in
animal models 266
11.5 Examples of disease models used in development of
preclinical vaccines in animal models 270
11.5.1 Influenza 270
11.5.2 Leishmaniasis 272
11.6 Conclusion 275
References 276
12. Vaccine human clinical trial
Bhawana Singh, Shyamali, Dharmendra Kumar Maurya, Rajiv Kumar,
Shashi Bhushan Chauhan, Shyam Lal Mudavath, Ram Niwas Meena,
Shyam Sundar, Om Prakash Singh
12.1 Introduction 281
12.2 Vaccine development and complexities 282
12.3 Human clinical trial 284
12.3.1 Phase I clinical trial 285
12.3.2 Phase II clinical trial 286
12.3.3 Phase III clinical trial 286
12.4 Vaccine license and approval process 286
12.5 Innovative strategy in vaccine development during times
of pandemics 287
12.6 COVID-19: reported clinical trials worldwide 289
12.7 Regulatory challenges 290