Skip to main content

Revisiting the Principles of Designing a Vaccine

  • Protocol
  • First Online:
Vaccine Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2410))

Abstract

Immune principles formulated by Jenner, Pasteur, and early immunologists served as fundamental propositions for vaccine discovery against many dreadful pathogens. However, decisive success in the form of an efficacious vaccine still eludes for diseases such as tuberculosis, leishmaniasis, and trypanosomiasis. Several antileishmanial vaccine trials have been undertaken in past decades incorporating live, attenuated, killed, or subunit vaccination, but the goal remains unmet. In light of the above facts, we have to reassess the principles of vaccination by dissecting factors associated with the hosts’ immune response. This chapter discusses the pathogen-associated perturbations at various junctures during the generation of the immune response which inhibits antigenic processing, presentation, or remodels memory T cell repertoire. This can lead to ineffective priming or inappropriate activation of memory T cells during challenge infection. Thus, despite a protective primary response, vaccine failure can occur due to altered immune environments in the presence of pathogens.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 299.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Zepp F (2016) Principles of vaccination. Methods Mol Biol 1403:57–84

    Article  PubMed  Google Scholar 

  2. Moser M, Leo O (2010) Key concepts in immunology. Vaccine 28(Suppl 3):C2–C13

    Article  CAS  PubMed  Google Scholar 

  3. Iborra S, Solana JC, Requena JM, Soto M (2018) Vaccine candidates against Leishmania under current research. Expert Rev Vaccines 17:323–334

    Article  CAS  PubMed  Google Scholar 

  4. McNicoll F, Drummelsmith J, Müller M et al (2006) A combined proteomic and transcriptomic approach to the study of stage differentiation in Leishmania infantum. Proteomics 6:3567–3581

    Article  CAS  PubMed  Google Scholar 

  5. Biyani N, Madhubala R (2012) Quantitative proteomic profiling of the promastigotes and the intracellular amastigotes of Leishmania donovani isolates identifies novel proteins having a role in Leishmania differentiation and intracellular survival. Biochim Biophys Acta 1824:1342–1350

    Article  CAS  PubMed  Google Scholar 

  6. Bhowmick S, Ravindran R, Ali N (2008) gp63 in stable cationic liposomes confers sustained vaccine immunity to susceptible BALB/c mice infected with Leishmania donovani. Infect Immun 76:1003–1015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. McMahon-Pratt D, Rodriguez D, Rodriguez JR et al (1993) Recombinant vaccinia viruses expressing GP46/M-2 protect against Leishmania infection. Infect Immun 61:3351–3359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Gurunathan S, Sacks DL, Brown DR et al (1997) Vaccination with DNA encoding the immunodominant LACK parasite antigen confers protective immunity to mice infected with Leishmania major. J Exp Med 186:1137–1147

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Melby PC, Yang J, Zhao W, Perez LE, Cheng J (2001) Leishmania donovani p36(LACK) DNA vaccine is highly immunogenic but not protective against experimental visceral leishmaniasis. Infect Immun 69:4719–4725

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Fernandes AP, Coelho EA, Machado-Coelho GL, Grimaldi G Jr, Gazzinelli RT (2012) Making an anti-amastigote vaccine for visceral leishmaniasis: rational, update and perspectives. Curr Opin Microbiol 15:476–485

    Article  CAS  PubMed  Google Scholar 

  11. Stäger S, Smith DF, Kaye PM (2000) Immunization with a recombinant stage-regulated surface protein from Leishmania donovani induces protection against visceral leishmaniasis. J Immunol 165:7064–7071

    Article  PubMed  Google Scholar 

  12. Elikaee S, Mohebali M, Rezaei S et al (2019) Leishmania major p27 gene knockout as a novel live attenuated vaccine candidate: protective immunity and efficacy evaluation against cutaneous and visceral leishmaniasis in BALB/c mice. Vaccine 37:3221–3228

    Article  CAS  PubMed  Google Scholar 

  13. Banerjee A, Bhattacharya P, Dagur PK et al (2018) Live attenuated Leishmania donovani Centrin gene-deleted parasites induce IL-23-dependent IL-17-protective immune response against visceral Leishmaniasis in a murine model. J Immunol 200:163–176

    Article  CAS  PubMed  Google Scholar 

  14. Velazquez C, DiPaolo R, Unanue ER (2001) Quantitation of lysozyme peptides bound to class II MHC molecules indicates very large differences in levels of presentation. J Immunol 166:5488–5494

    Article  CAS  PubMed  Google Scholar 

  15. Croft NP, Smith SA, Wong YC et al (2013) Kinetics of antigen expression and epitope presentation during virus infection. PLoS Pathog 9:e1003129

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Tenzer S, Wee E, Burgevin A et al (2009) Antigen processing influences HIV-specific cytotoxic T lymphocyte immunodominance. Nat Immunol 10:636–646

    Article  CAS  PubMed  Google Scholar 

  17. Boulanger D, Eccleston RC, Phillips A (2018) A mechanistic model for predicting cell surface presentation of competing peptides by MHC class I molecules. Front Immunol 9:1538

    Article  PubMed  PubMed Central  Google Scholar 

  18. Rollenhagen C, Sörensen M, Rizos K, Hurvitz R, Bumann D (2004) Antigen selection based on expression levels during infection facilitates vaccine development for an intracellular pathogen. Proc Natl Acad Sci U S A 101:8739–8744

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Abelin JG, Keskin DB, Sarkizova S et al (2017) Mass spectrometry profiling of HLA-associated peptidomes in mono-allelic cells enables more accurate epitope prediction. Immunity 46:315–326

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Chen B, Khodadoust MS, Olsson N et al (2019) Predicting HLA class II antigen presentation through integrated deep learning. Nat Biotechnol 37:1332–1343

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Sarkizova S, Klaeger S, Le PM et al (2020) A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nat Biotechnol 38:199–209

    Article  CAS  PubMed  Google Scholar 

  22. Milner E, Barnea E, Beer I, Admon A (2006) The turnover kinetics of major histocompatibility complex peptides of human cancer cells. Mol Cell Proteomics 5:357–365

    Article  CAS  PubMed  Google Scholar 

  23. Akya A, Farasat A, Ghadiri K, Rostamian M (2019) Identification of HLA-I restricted epitopes in six vaccine candidates of Leishmania tropica using immunoinformatics and molecular dynamics simulation approaches. Infect Genet Evol 75:103953

    Article  CAS  PubMed  Google Scholar 

  24. Kima PE, Soong L, Chicharro C et al (1996) Leishmania-infected macrophages sequester endogenously synthesized parasite antigens from presentation to CD4+ T cells. Eur J Immunol 26:3163–3169

    Article  CAS  PubMed  Google Scholar 

  25. Houde M, Bertholet S, Gagnon E et al (2003) Phagosomes are competent organelles for antigen cross-presentation. Nature 425:402–406

    Article  CAS  PubMed  Google Scholar 

  26. Wolfram M, Fuchs M, Wiese M, Stierhof YD, Overath P (1996) Antigen presentation by Leishmania mexicana-infected macrophages: activation of helper T cells by a model parasite antigen secreted into the parasitophorous vacuole or expressed on the amastigote surface. Eur J Immunol 26:3153–3162

    Article  CAS  PubMed  Google Scholar 

  27. Wolfram M, Ilg T, Mottram JC, Overath P (1995) Antigen presentation by Leishmania mexicana-infected macrophages: activation of helper T cells specific for amastigote cysteine proteinases requires the intracellular killing of the parasites. Eur J Immunol 25:1094–1100

    Article  CAS  PubMed  Google Scholar 

  28. Dupé A, Dumas C, Papadopoulou B (2015) Differential subcellular localization of Leishmania Alba-domain proteins throughout the parasite development. PLoS One 10:e0137243

    Article  PubMed  PubMed Central  Google Scholar 

  29. Gregg B, Dzierszinski F, Tait E, Jordan KA, Hunter CA, Roos DS (2011) Subcellular antigen location influences T-cell activation during acute infection with toxoplasma gondii. PLoS One 6:e22936

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Rush C, Mitchell T, Garside P (2002) Efficient priming of CD4+ and CD8+ T cells by DNA vaccination depends on appropriate targeting of sufficient levels of immunologically relevant antigen to appropriate processing pathways. J Immunol 169:4951–4960

    Article  PubMed  Google Scholar 

  31. Bertholet S, Debrabant A, Afrin F et al (2005) Antigen requirements for efficient priming of CD8+ T cells by Leishmania major-infected dendritic cells. Infect Immun 73:6620–6628

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Courret N, Fréhel C, Gouhier N et al (2002) Biogenesis of Leishmania-harbouring parasitophorous vacuoles following phagocytosis of the metacyclic promastigote or amastigote stages of the parasites. J Cell Sci 115:2303–2316

    Article  CAS  PubMed  Google Scholar 

  33. Kumar GA, Karmakar J, Mandal C, Chattopadhyay A (2019) Leishmania donovani internalizes into host cells via caveolin-mediated endocytosis. Sci Rep 9:12636

    Article  PubMed  PubMed Central  Google Scholar 

  34. Burgdorf S, Kurts C (2008) Endocytosis mechanisms and the cell biology of antigen presentation. Curr Opin Immunol 20:89–95

    Article  CAS  PubMed  Google Scholar 

  35. Liu D, Uzonna JE (2012) The early interaction of Leishmania with macrophages and dendritic cells and its influence on the host immune response. Front Cell Infect Microbiol 2:83

    Article  PubMed  PubMed Central  Google Scholar 

  36. Dey R, Khan S, Pahari S, Srivastava N, Jadhav M, Saha B (2007) Functional paradox in host-pathogen interaction dictates the fate of parasites. Future Microbiol 2:425–437

    Article  CAS  PubMed  Google Scholar 

  37. Tomiotto-Pellissier F, Bortoleti BTDS, Assolini JP et al (2018) Macrophage polarization in Leishmaniasis: broadening horizons. Front Immunol 9:2529

    Article  PubMed  PubMed Central  Google Scholar 

  38. Matheoud D, Moradin N, Bellemare-Pelletier A et al (2013) Leishmania evades host immunity by inhibiting antigen cross-presentation through direct cleavage of the SNARE VAMP8. Cell Host Microbe 14:15–25

    Article  CAS  PubMed  Google Scholar 

  39. Moradin N, Descoteaux A (2012) Leishmania promastigotes: building a safe niche within macrophages. Front Cell Infect Microbiol 2:121

    Article  PubMed  PubMed Central  Google Scholar 

  40. Matte C, Casgrain PA, SĂ©guin O, Moradin N, Hong WJ, Descoteaux A (2016) Leishmania major promastigotes evade LC3-associated phagocytosis through the action of GP63. PLoS Pathog 12:e1005690

    Article  PubMed  PubMed Central  Google Scholar 

  41. Matte C, Descoteaux A (2016) Exploitation of the host cell membrane fusion machinery by Leishmania is part of the infection process. PLoS Pathog 12:e1005962

    Article  PubMed  PubMed Central  Google Scholar 

  42. Zhang T, Maekawa Y, Sakai T et al (2001) Treatment with cathepsin L inhibitor potentiates Th2-type immune response in Leishmania major-infected BALB/c mice. Int Immunol 13:975–982

    Article  CAS  PubMed  Google Scholar 

  43. Arango Duque G, Fukuda M, Descoteaux A (2013) Synaptotagmin XI regulates phagocytosis and cytokine secretion in macrophages. J Immunol 190:1737–1745

    Article  CAS  PubMed  Google Scholar 

  44. Czibener C, Sherer NM, Becker SM et al (2006) Ca2+ and synaptotagmin VII-dependent delivery of lysosomal membrane to nascent phagosomes. J Cell Biol 174:997–1007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. da Silva VT, Arango Duque G, Ory K, Gontijo CM, Soares RP, Descoteaux A (2019) Leishmania braziliensis: strain-specific modulation of phagosome maturation. Front Cell Infect Microbiol 9:319

    Article  Google Scholar 

  46. van Kasteren SI, Overkleeft HS (2014) Endo-lysosomal proteases in antigen presentation. Curr Opin Chem Biol 23:8–15

    Article  PubMed  Google Scholar 

  47. Bühling F, Waldburg N, Reisenauer A et al (2004) Lysosomal cysteine proteases in the lung: role in protein processing and immunoregulation. Eur Respir J 23:620–628

    Article  PubMed  Google Scholar 

  48. Matte C, Descoteaux A (2010) Leishmania donovani amastigotes impair gamma interferon-induced STAT1alpha nuclear translocation by blocking the interaction between STAT1alpha and importin-alpha5. Infect Immun 78:3736–3743

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Rudensky A, Beers C (2006) Lysosomal cysteine proteases and antigen presentation. Ernst Schering Res Found Workshop (56):81–95

    Google Scholar 

  50. Lemaire R, Huet G, Zerimech F et al (1997) Selective induction of the secretion of cathepsins B and L by cytokines in synovial fibroblast-like cells. Br J Rheumatol 36:735–743

    Article  CAS  PubMed  Google Scholar 

  51. Müller S, Faulhaber A, Sieber C et al (2014) The endolysosomal cysteine cathepsins L and K are involved in macrophage-mediated clearance of Staphylococcus aureus and the concomitant cytokine induction. FASEB J 28:162–175

    Article  PubMed  Google Scholar 

  52. Maekawa Y, Himeno K, Ishikawa H et al (1998) Switch of CD4+ T cell differentiation from Th2 to Th1 by treatment with cathepsin B inhibitor in experimental leishmaniasis. J Immunol 161:2120–2127

    CAS  PubMed  Google Scholar 

  53. Gonzalez-Leal IJ, Röger B, Schwarz A et al (2014) Cathepsin B in antigen-presenting cells controls mediators of the Th1 immune response during Leishmania major infection. PLoS Negl Trop Dis 8:e3194

    Article  PubMed  PubMed Central  Google Scholar 

  54. Onishi K, Li Y, Ishii K et al (2004) Cathepsin L is crucial for a Th1-type immune response during Leishmania major infection. Microbes Infect 6:468–474

    Article  CAS  PubMed  Google Scholar 

  55. MĂĽnz C (2012) Antigen processing for MHC class II presentation via autophagy. Front Immunol 3:9

    Article  PubMed  PubMed Central  Google Scholar 

  56. Roy S, Mukhopadhyay D, Mukherjee S et al (2015) A defective oxidative burst and impaired antigen presentation are hallmarks of human visceral Leishmaniasis. J Clin Immunol 35:56–67

    Article  CAS  PubMed  Google Scholar 

  57. Antoine JC, Lang T, Prina E, Courret N, Hellio R (1999) H-2M molecules, like MHC class II molecules, are targeted to parasitophorous vacuoles of Leishmania-infected macrophages and internalized by amastigotes of L. amazonensis and L. mexicana. J Cell Sci 112:2559–2570

    Article  CAS  PubMed  Google Scholar 

  58. Costa SS, Fornazim MC, Nowill AE, Giorgio S (2018) Leishmania amazonensis induces modulation of costimulatory and surface marker molecules in human macrophages. Parasite Immunol 40:e12519

    Article  CAS  PubMed  Google Scholar 

  59. Figueiredo AB, Serafim TD, Marques-da-Silva EA, Meyer-Fernandes JR, Afonso LC (2012) Leishmania amazonensis impairs DC function by inhibiting CD40 expression via A2B adenosine receptor activation. Eur J Immunol 42:1203–1215

    Article  CAS  PubMed  Google Scholar 

  60. Moudgil KD, Sercarz EE (2005) Understanding crypticity is the key to revealing the pathogenesis of autoimmunity. Trends Immunol 26:355–359

    Article  CAS  PubMed  Google Scholar 

  61. Blum JS, Ma C, Kovats S (1997) Antigen-presenting cells and the selection of immunodominant epitopes. Crit Rev Immunol 17:411–417

    CAS  PubMed  Google Scholar 

  62. Ma C, Whiteley PE, Cameron PM et al (1999) Role of APC in the selection of immunodominant T cell epitopes. J Immunol 163:6413–6423

    CAS  PubMed  Google Scholar 

  63. Kim A, Hartman IZ, Poore B et al (2014) Divergent paths for the selection of immunodominant epitopes from distinct antigenic sources. Nat Commun 5:5369

    Article  CAS  PubMed  Google Scholar 

  64. Kelly BL, Locksley RM (2004) The Leishmania major LACK antigen with an immunodominant epitope at amino acids 156 to 173 is not required for early Th2 development in BALB/c mice. Infect Immun 72:6924–6931

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Feliu V, Vasseur V, Grover HS et al (2013) Location of the CD8 T cell epitope within the antigenic precursor determines immunogenicity and protection against the toxoplasma gondii parasite. PLoS Pathog 9:e1003449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Dominguez MR, Silveira EL, de Vasconcelos JR et al (2011) Subdominant/cryptic CD8 T cell epitopes contribute to resistance against experimental infection with a human protozoan parasite. PLoS One 6:e22011

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Fruth U, Solioz N, Louis JA (1993) Leishmania major interferes with antigen presentation by infected macrophages. J Immunol 150:1857–1864

    CAS  PubMed  Google Scholar 

  68. Lang T, de Chastellier C, Frehel C et al (1994) Distribution of MHC class I and of MHC class II molecules in macrophages infected with Leishmania amazonensis. J Cell Sci 107:69–82

    Article  CAS  PubMed  Google Scholar 

  69. Storni T, Bachmann MF (2004) Loading of MHC class I and II presentation pathways by exogenous antigens: a quantitative in vivo comparison. J Immunol 172:6129–6135

    Article  CAS  PubMed  Google Scholar 

  70. Simon A, Zs D, Rajnavölgyi E, Simon I (2000) Function-related regulation of the stability of MHC proteins. Biophys J 79:2305–2313

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Sant AJ, Chaves FA, Jenks SA et al (2005) The relationship between immunodominance, DM editing, and the kinetic stability of MHC class II: peptide complexes. Immunol Rev 207:261–278

    Article  CAS  PubMed  Google Scholar 

  72. Nanda NK, Sant AJ (2000) DM determines the cryptic and immunodominant fate of T cell epitopes. J Exp Med 192:781–788

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. McMahan RH, McWilliams JA, Jordan KR, Dow SW, Wilson DB, Slansky JE (2006) Relating TCR-peptide-MHC affinity to immunogenicity for the design of tumor vaccines. J Clin Invest 116:2543–2551

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Schneidman-Duhovny D, Khuri N, Dong GQ et al (2018) Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition. PLoS One 13:e0206654

    Article  PubMed  PubMed Central  Google Scholar 

  75. Paul S, Weiskopf D, Angelo MA, Sidney J, Peters B, Sette A (2013) HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity. J Immunol 191:5831–5839

    Article  CAS  PubMed  Google Scholar 

  76. Zhu H, Liu K, Cerny J, Imoto T, Moudgil KD (2005) Insertion of the dibasic motif in the flanking region of a cryptic self-determinant leads to activation of the epitope-specific T cells. J Immunol 175:2252–2260

    Article  CAS  PubMed  Google Scholar 

  77. Sadegh-Nasseri S, Kim A (2019) Selection of immunodominant epitopes during antigen processing is hierarchical. Mol Immunol 113:115–119

    Article  CAS  PubMed  Google Scholar 

  78. Roy K, Naskar K, Ghosh M, Roy S (2014) Class II MHC/peptide interaction in Leishmania donovani infection: implications in vaccine design. J Immunol 192:5873–5880

    Article  CAS  PubMed  Google Scholar 

  79. Roy K, Mandloi S, Chakrabarti S, Roy S (2016) Cholesterol corrects altered conformation of MHC-II protein in Leishmania donovani infected macrophages: implication in therapy. PLoS Negl Trop Dis 10:e0004710

    Article  PubMed  PubMed Central  Google Scholar 

  80. Dustin ML (2014) The immunological synapse. Cancer Immunol Res 2:1023–1033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Meier CL, Svensson M, Kaye PM (2003) Leishmania-induced inhibition of macrophage antigen presentation analyzed at the single-cell level. J Immunol 171:6706–6713

    Article  CAS  PubMed  Google Scholar 

  82. Resende M, Moreira D, Augusto J, Cunha J, Neves B, Cruz MT, Estaquier J, Cordeiro-da-Silva A, Silvestre R (2013) Leishmania-infected MHC class II high dendritic cells polarize CD4+ T cells toward a nonprotective T-bet+ IFN-γ+ IL-10+ phenotype. J Immunol 191:262–273

    Article  CAS  PubMed  Google Scholar 

  83. Freiberg BA, Kupfer H, Maslanik W et al (2002) Staging and resetting T cell activation in SMACs. Nat Immunol 3:911–917

    Article  CAS  PubMed  Google Scholar 

  84. Lee KH, Dinner AR, Tu C et al (2003) The immunological synapse balances T cell receptor signaling and degradation. Science 302:1218–1222

    Article  CAS  PubMed  Google Scholar 

  85. Alarcón B, Mestre D, Martínez-Martín N (2011) The immunological synapse: a cause or consequence of T-cell receptor triggering? Immunology 133:420–425

    Article  PubMed  PubMed Central  Google Scholar 

  86. Smith A, Stanley P, Jones K, Svensson L, McDowall A, Hogg N (2007) The role of the integrin LFA-1 in T-lymphocyte migration. Immunol Rev 218:135–146

    Article  CAS  PubMed  Google Scholar 

  87. Wonerow P, Watson SP (2001) The transmembrane adapter LAT plays a central role in immune receptor signaling. Oncogene 20:6273–6283

    Article  CAS  PubMed  Google Scholar 

  88. Huang SC, Tsai HF, Tzeng HT, Liao HJ, Hsu PN (2011) Lipid raft assembly and Lck recruitment in TRAIL costimulation mediates NF-κB activation and T cell proliferation. J Immunol 186:931–939

    Article  CAS  PubMed  Google Scholar 

  89. Rub A, Dey R, Jadhav M et al (2009) Cholesterol depletion associated with Leishmania major infection alters macrophage CD40 signalosome composition and effector function. Nat Immunol 10:273–280

    Article  CAS  PubMed  Google Scholar 

  90. Chakraborty D, Banerjee S, Sen A, Banerjee KK, Das P, Roy S (2005) Leishmania donovani affects antigen presentation of macrophage by disrupting lipid rafts. J Immunol 175:3214–3224

    Article  CAS  PubMed  Google Scholar 

  91. Banerjee S, Ghosh J, Sen S et al (2009) Designing therapies against experimental visceral leishmaniasis by modulating the membrane fluidity of antigen-presenting cells. Infect Immun 77:2330–2342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Veras PST, Ramos PIP, de Menezes JPB (2018) In search of biomarkers for pathogenesis and control of Leishmaniasis by global analyses of Leishmania-infected macrophages. Front Cell Infect Microbiol 8:326

    Article  PubMed  PubMed Central  Google Scholar 

  93. Dustin ML, Long EO (2010) Cytotoxic immunological synapses. Immunol Rev 235:24–34

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Tourret M, Guégan S, Chemin K et al (2010) T cell polarity at the immunological synapse is required for CD154-dependent IL-12 secretion by dendritic cells. J Immunol 185:6809–6818

    Article  CAS  PubMed  Google Scholar 

  95. Yokosuka T, Saito T (2009) Dynamic regulation of T-cell costimulation through TCR-CD28 microclusters. Immunol Rev 229:27–40

    Article  CAS  PubMed  Google Scholar 

  96. Brzostek J, Gascoigne NR, Rybakin V (2016) Cell type-specific regulation of immunological synapse dynamics by B7 ligand recognition. Front Immunol 7:24

    Article  PubMed  PubMed Central  Google Scholar 

  97. Kaech SM, Wherry EJ (2007) Heterogeneity and cell-fate decisions in effector and memory CD8+ T cell differentiation during viral infection. Immunity 27:393–405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. von Essen MR, Kongsbak M, Geisler C (2012) Mechanisms behind functional avidity maturation in T cells. Clin Dev Immunol 2012:163453

    Google Scholar 

  99. Langenkamp A, Casorati G, Garavaglia C, Dellabona P, Lanzavecchia A, Sallusto F (2002) T cell priming by dendritic cells: thresholds for proliferation, differentiation and death and intraclonal functional diversification. Eur J Immunol 32:2046–2054

    Article  CAS  PubMed  Google Scholar 

  100. Hirahara K, Poholek A, Vahedi G et al (2013) Mechanisms underlying helper T-cell plasticity: implications for immune-mediated disease. J Allergy Clin Immunol 131:1276–1287

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Ivanova EA, Orekhov AN (2015) T helper lymphocyte subsets and plasticity in autoimmunity and cancer: an overview. Biomed Res Int 2015:327470

    Article  PubMed  PubMed Central  Google Scholar 

  102. Muranski P, Restifo NP (2013) Essentials of Th17 cell commitment and plasticity. Blood 121:2402–2414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Schmitt E, Klein M, Bopp T (2014) Th9 cells, new players in adaptive immunity. Trends Immunol 35:61–68

    Article  CAS  PubMed  Google Scholar 

  104. Selin LK, Welsh RM (2004) Plasticity of T cell memory responses to viruses. Immunity 20:5–16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Lees JR, Farber DL (2010) Generation, persistence and plasticity of CD4 T-cell memories. Immunology 130:463–470

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Schwartz RH (2003) T cell anergy. Annu Rev Immunol 21:305–334

    Article  CAS  PubMed  Google Scholar 

  107. Pinheiro RO, Pinto EF, Benedito AB, Lopes UG, Rossi-Bergmann B (2004) The T-cell anergy induced by Leishmania amazonensis antigens is related with defective antigen presentation and apoptosis. An Acad Bras Cienc 76:519–527

    Article  CAS  PubMed  Google Scholar 

  108. Funeshima N, Fujino M, Kitazawa Y et al (2005) Inhibition of allogeneic T-cell responses by dendritic cells expressing transduced indoleamine 2,3-dioxygenase. J Gene Med 7:565–575

    Article  CAS  PubMed  Google Scholar 

  109. Sakaguchi S, Wing K, Yamaguchi T (2009) Dynamics of peripheral tolerance and immune regulation mediated by Treg. Eur J Immunol 39:2331–2336

    Article  CAS  PubMed  Google Scholar 

  110. Wing K, Yamaguchi T, Sakaguchi S (2011) Cell-autonomous and -non-autonomous roles of CTLA-4 in immune regulation. Trends Immunol 32:428–433

    Article  CAS  PubMed  Google Scholar 

  111. Andris F, Denanglaire S, de Mattia F, Urbain J, Leo O (2004) Naive T cells are resistant to anergy induction by anti-CD3 antibodies. J Immunol 173:3201–3208

    Article  CAS  PubMed  Google Scholar 

  112. Gautam S, Kumar R, Singh N et al (2014) CD8 T cell exhaustion in human visceral leishmaniasis. J Infect Dis 209:290–299

    Article  CAS  PubMed  Google Scholar 

  113. Yi JS, Cox MA, Zajac AJ (2010) T-cell exhaustion: characteristics, causes, and conversion. Immunology 129:474–481

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Wherry EJ (2011) T cell exhaustion. Nat Immunol 12:492–499

    Article  CAS  PubMed  Google Scholar 

  115. Habib S, El Andaloussi A, Elmasry K et al (2018) PDL-1 blockade prevents T cell exhaustion, inhibits autophagy, and promotes clearance of Leishmania donovani. Infect Immun 86:e00019–e00018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Basmaciyan L, Casanova M (2019) Cell death in Leishmania. La mort cellulaire chez Leishmania. Parasite 26:71

    Article  PubMed  PubMed Central  Google Scholar 

  117. Basmaciyan L, Robinson DR, Azas N, Casanova M (2019) (De)glutamylation and cell death in Leishmania parasites. PLoS Negl Trop Dis 13:e0007264

    Article  PubMed  PubMed Central  Google Scholar 

  118. Kalia V, Sarkar S, Ahmed R (2010) CD8 T-cell memory differentiation during acute and chronic viral infections. Adv Exp Med Biol 684:79–95

    Article  CAS  PubMed  Google Scholar 

  119. Radosević K, Rodriguez A, Lemckert A, Goudsmit J (2009) Heterologous prime-boost vaccinations for poverty-related diseases: advantages and future prospects. Expert Rev Vaccines 8:577–592

    Article  PubMed  Google Scholar 

  120. Martin MD, Badovinac VP (2014) Influence of time and number of antigen encounters on memory CD8 T cell development. Immunol Res 59:35–44

    Article  CAS  PubMed  Google Scholar 

  121. Pearce EL, Shen H (2006) Making sense of inflammation, epigenetics, and memory CD8+ T-cell differentiation in the context of infection. Immunol Rev 211:197–202

    Article  CAS  PubMed  Google Scholar 

  122. Serruto D, Rappuoli R (2006) Post-genomic vaccine development. FEBS Lett 580:2985–2992

    Article  CAS  PubMed  Google Scholar 

  123. Mora M, Veggi D, Santini L et al (2003) Reverse vaccinology. Drug Discov Today 8:459–464

    Article  CAS  PubMed  Google Scholar 

  124. DeLisi C, Berzofsky JA (1985) T-cell antigenic sites tend to be amphipathic structures. Proc Natl Acad Sci U S A 82:7048–7052

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. He Y, Rappuoli R, De Groot AS, Chen RT (2010) Emerging vaccine informatics. J Biomed Biotechnol 2010:218590

    PubMed  Google Scholar 

  126. De Groot AS (2006) Immunomics: discovering new targets for vaccines and therapeutics. Drug Discov Today 11:203–209

    Article  PubMed  Google Scholar 

  127. McMurry JA, Gregory SH, Moise L et al (2007) Diversity of Francisella tularensis Schu4 antigens recognized by T lymphocytes after natural infections in humans: identification of candidate epitopes for inclusion in a rationally designed tularemia vaccine. Vaccine 25:3179–3191

    Article  CAS  PubMed  Google Scholar 

  128. Rappuoli R (2000) Reverse vaccinology. Curr Opin Microbiol 3:445–450

    Article  CAS  PubMed  Google Scholar 

  129. Moxon R, Reche PA, Rappuoli R (2019) Editorial: reverse vaccinology. Front Immunol 10:2776

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Pizza M, Scarlato V, Masignani V (2000) Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 287:1816–1820

    Article  CAS  PubMed  Google Scholar 

  131. Madden DR (1995) The three-dimensional structure of peptide-MHC complexes. Annu Rev Immunol 13:587–622

    Article  CAS  PubMed  Google Scholar 

  132. Harris PE (1994) Self-peptides bound to HLA molecules. Crit Rev Immunol 14:61–87

    CAS  PubMed  Google Scholar 

  133. E Silva R, Ferreira LF, Hernandes MZ et al (2016) Combination of in silico methods in the search for potential CD4(+) and CD8(+) T cell epitopes in the proteome of Leishmania braziliensis. Front Immunol 7:327

    Article  PubMed Central  Google Scholar 

  134. E Silva RF, de Oliveira BC, da Silva AA et al (2020) Immunogenicity of potential CD4+ and CD8+ T cell epitopes derived from the proteome of Leishmania braziliensis. Front Immunol 10:3145

    Article  PubMed  PubMed Central  Google Scholar 

  135. Bordbar A, Bagheri KP, Ebrahimi S et al (2020) Bioinformatics analyses of immunogenic T-cell epitopes of LeIF and PpSP15 proteins from Leishmania major and sand fly saliva used as model antigens for the design of a multi-epitope vaccine to control leishmaniasis. Infect Genet Evol 80:104189

    Article  CAS  PubMed  Google Scholar 

  136. Gfeller D, Bassani-Sternberg M (2018) Predicting antigen presentation-what could we learn from a million peptides? Front Immunol 9:1716

    Article  PubMed  PubMed Central  Google Scholar 

  137. Oyarzun P, Ellis JJ, Gonzalez-Galarza FF et al (2015) A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: application to emerging infectious diseases. Vaccine 33:1267–1273

    Article  CAS  PubMed  Google Scholar 

  138. Dhanda SK, Vir P, Raghava GP (2013) Designing of interferon-gamma inducing MHC class-II binders. Biol Direct 8:30

    Article  PubMed  PubMed Central  Google Scholar 

  139. Shey RA, Ghogomu SM, Esoh KK et al (2019) In-silico design of a multi-epitope vaccine candidate against onchocerciasis and related filarial diseases. Sci Rep 9:4409

    Article  PubMed  PubMed Central  Google Scholar 

  140. Tettelin H, Medini D, Donati C, Masignani V (2006) Towards a universal group B streptococcus vaccine using multistrain genome analysis. Expert Rev Vaccines 5:687–694

    Article  CAS  PubMed  Google Scholar 

  141. Mora M, Donati C, Medini D et al (2006) Microbial genomes and vaccine design: refinements to the classical reverse vaccinology approach. Curr Opin Microbiol 9:532–536

    Article  CAS  PubMed  Google Scholar 

  142. Naz K, Naz A, Ashraf ST, Rizwan M, Ahmad J, Baumbach J, Ali A (2019) PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. BMC Bioinformatics 20:123

    Article  PubMed  PubMed Central  Google Scholar 

  143. Delcher AL, Harmon D, Kasif S et al (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Tanizawa Y, Fujisawa T, Nakamura Y (2018) DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 34:1037–1039

    Article  CAS  PubMed  Google Scholar 

  145. Issac B, Raghava GP (2004) EGPred: prediction of eukaryotic genes using ab initio methods after combining with sequence similarity approaches. Genome Res 14:1756–1766

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Zutshi S, Kumar S, Chauhan P et al (2019) Anti-leishmanial vaccines: assumptions, approaches, and annulments. Vaccines (Basel) 7:156

    Article  CAS  Google Scholar 

  147. Yu NY, Wagner JR, Laird MR et al (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26:1608–1615

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Mooney C, Wang YH, Pollastri G (2011) SCLpred: protein subcellular localization prediction by N-to-1 neural networks. Bioinformatics 27:2812–2819

    Article  CAS  PubMed  Google Scholar 

  149. Gupta S, Madhu MK, Sharma AK et al (2016) ProInflam: a webserver for the prediction of proinflammatory antigenicity of peptides and proteins. J Transl Med 14:178

    Article  PubMed  PubMed Central  Google Scholar 

  150. Zhou X, Yin R, Kwoh CK et al (2018) A context-free encoding scheme of protein sequences for predicting antigenicity of diverse influenza a viruses. BMC Genomics 19:936

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Doytchinova IA, Flower DR (2007) VaxiJen: a server for prediction of protective antigens, tumour antigens, and subunit vaccines. BMC Bioinformatics 8:4

    Article  PubMed  PubMed Central  Google Scholar 

  152. Magnan CN, Zeller M, Kayala MA (2010) High-throughput prediction of protein antigenicity using protein microarray data. Bioinformatics 26:2936–2943

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Dikhit MR, Vijayamahantesh Kumar A, Amit A (2018) Mining the proteome of Leishmania donovani for the development of novel MHC class I restricted epitope for the control of visceral Leishmaniasis. J Cell Biochem 119:378–391

    Article  CAS  PubMed  Google Scholar 

  154. Kashyap M, Jaiswal V, Farooq U (2017) Prediction and analysis of promiscuous T cell-epitopes derived from the vaccine candidate antigens of Leishmania donovani binding to MHC class-II alleles using in silico approach. Infect Genet Evol 53:107–115

    Article  CAS  PubMed  Google Scholar 

  155. John L, John GJ, Kholia T (2012) A reverse vaccinology approach for the identification of potential vaccine candidates from Leishmania spp. Appl Biochem Biotechnol 167(5):1340–1350

    Article  CAS  PubMed  Google Scholar 

  156. Khatoon N, Pandey RK, Prajapati VK (2017) Exploring Leishmania secretory proteins to design B and T cell multi-epitope subunit vaccine using immunoinformatics approach. Sci Rep 7:8285

    Article  PubMed  PubMed Central  Google Scholar 

  157. Khatoon N, Pandey RK, Ojha R et al (2019) Exploratory algorithm to devise multi-epitope subunit vaccine by investigating Leishmania donovani membrane proteins. J Biomol Struct Dyn 37:2381–2393

    Article  CAS  PubMed  Google Scholar 

  158. Singh G, Pritam M, Banerjee M et al (2019) Genome-based screening of epitope ensemble vaccine candidates against dreadful visceral leishmaniasis using immunoinformatics approach. Microb Pathog 136:103704

    Article  CAS  PubMed  Google Scholar 

  159. Khan M, Ami JQ, Faisal K et al (2020) An immunoinformatic approach driven by experimental proteomics: in silico design of a subunit candidate vaccine targeting secretory proteins of Leishmania donovani amastigotes. Parasit Vectors 13:196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Vakili B, Nezafat N, Hatam GR et al (2018) Proteome-scale identification of Leishmania infantum for novel vaccine candidates: a hierarchical subtractive approach. Comput Biol Chem 72:16–25

    Article  CAS  PubMed  Google Scholar 

  161. Oliveira MP, Martins VT, Santos T et al (2018) Small myristoylated protein-3, identified as a potential virulence factor in Leishmania amazonensis, proves to be a protective antigen against visceral Leishmaniasis. Int J Mol Sci 19:129

    Article  PubMed Central  Google Scholar 

  162. Hamrouni S, Bras-Gonçalves R, Kidar A et al (2020) Design of multi-epitope peptides containing HLA class-I and class-II-restricted epitopes derived from immunogenic Leishmania proteins, and evaluation of CD4+ and CD8+ T cell responses induced in cured cutaneous leishmaniasis subjects. PLoS Negl Trop Dis 14:e0008093

    Article  PubMed  PubMed Central  Google Scholar 

  163. Bagnoli F, Baudner B, Mishra RP et al (2011) Designing the next generation of vaccines for global public health. OMICS 15:545–566

    Article  CAS  PubMed  Google Scholar 

  164. Gandhi A, Balmer P, York LJ (2016) Characteristics of a new meningococcal serogroup B vaccine, bivalent rLP2086 (MenB-FHbp; Trumenba®). Postgrad Med 128:548–556

    Article  PubMed  Google Scholar 

  165. Hornburg D, Kruse T, Anderl F et al (2019) A mass spectrometry guided approach for the identification of novel vaccine candidates in gram-negative pathogens. Sci Rep 9:17401

    Article  PubMed  PubMed Central  Google Scholar 

  166. Nilsson Bark SK, Ahmad R, Dantzler K (2018) Quantitative proteomic profiling reveals novel plasmodium falciparum surface antigens and possible vaccine candidates. Mol Cell Proteomics 17:43–60

    Article  CAS  PubMed  Google Scholar 

  167. Olivier M, Fernandez-Prada C (2019) Leishmania and its exosomal pathway: a novel direction for vaccine development. Future Microbiol 14:559–561

    Article  CAS  PubMed  Google Scholar 

  168. Silverman JM, Reiner NE (2012) Leishmania exosomes deliver preemptive strikes to create an environment permissive for early infection. Front Cell Infect Microbiol 1:26

    Article  PubMed  PubMed Central  Google Scholar 

  169. Pérez-Cabezas B, Santarém N, Cecílio P et al (2018) More than just exosomes: distinct Leishmania infantum extracellular products potentiate the establishment of infection. J Extracell Vesicles 8:1541708

    Article  PubMed  PubMed Central  Google Scholar 

  170. MagalhĂŁes RD, Duarte MC, Mattos EC et al (2014) Identification of differentially expressed proteins from Leishmania amazonensis associated with the loss of virulence of the parasites. PLoS Negl Trop Dis 8:e2764

    Article  PubMed  PubMed Central  Google Scholar 

  171. Jha MK, Sarode AY, Bodhale N et al (2020) Development and characterization of an Avirulent Leishmania major strain. J Immunol 204:2734–2753

    Article  CAS  PubMed  Google Scholar 

  172. Brobey RK, Mei FC, Cheng X et al (2006) Comparative two-dimensional gel electrophoresis maps for promastigotes of Leishmania amazonensis and Leishmania major. Braz J Infect Dis 10:1–6

    Article  PubMed  Google Scholar 

  173. Misra P, Tandon R, Basak T et al (2020) Purified splenic amastigotes of Leishmania donovani-Immunoproteomic approach for exploring Th1 stimulatory polyproteins. Parasite Immunol 42:e12729

    Article  CAS  PubMed  Google Scholar 

  174. Cotugno N, Ruggiero A, Santilli V et al (2019) OMIC technologies and vaccine development: from the identification of vulnerable individuals to the formulation of invulnerable vaccines. J Immunol Res 2019:8732191

    Article  PubMed  PubMed Central  Google Scholar 

  175. Dunston CR, Herbert R, Griffiths HR (2015) Improving T cell-induced response to subunit vaccines: opportunities for a proteomic systems approach. J Pharm Pharmacol 67:290–299

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Zutshi, S., Kumar, S., Chauhan, P., Saha, B. (2022). Revisiting the Principles of Designing a Vaccine. In: Thomas, S. (eds) Vaccine Design. Methods in Molecular Biology, vol 2410. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1884-4_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-1884-4_3

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1883-7

  • Online ISBN: 978-1-0716-1884-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics