Time for T? Immunoinformatics addresses vaccine design for neglected tropical and emerging infectious diseases

Expert Review of Vaccines

Volumn 14, Issue 1, 2014, Pages 21-35

  Terry, Frances E ^a   Moise, Leonard ^a,b   Martin, Rebecca F ^a   Torres, Melissa ^c   Pilotte, Nils ^c   Williams, Steven A ^c   De Groot, Anne S ^a,b  

^a EpiVax Inc   (United States)

^b UNIVERSITY OF RHODE ISLAND   (United States)

^c SMITH COLLEGE   (United States)

Author keywords

Brugia malayi; computational vaccinology; EID; EpiMatrix; filarial; immunogenicity; immunoinformatics; immunomics; JanusMatrix; MHC; NTD; T cell; TCR; tregitope

Indexed keywords

EPITOPE; VACCINE;

ADJUVANT THERAPY; ALGORITHM; B LYMPHOCYTE; CONSENSUS SEQUENCE; DRUG DELIVERY SYSTEM; DRUG DESIGN; EPITOPE MAPPING; GENOME; HUMAN; IMMUNE RESPONSE; IMMUNOGENICITY; IMMUNOINFORMATICS; INFECTION; IVAX APPROACH; MEDICAL INFORMATICS; NEGLECTED DISEASE; NONHUMAN; REVIEW; T LYMPHOCYTE; TROPICAL DISEASE; BIOLOGY; COMMUNICABLE DISEASES, EMERGING; GENETICS; GENOMICS; IMMUNOLOGY; ISOLATION AND PURIFICATION; NEGLECTED DISEASES; PROCEDURES; TROPIC CLIMATE;

COMMUNICABLE DISEASES, EMERGING; COMPUTATIONAL BIOLOGY; GENOMICS; HUMANS; NEGLECTED DISEASES; TROPICAL CLIMATE; VACCINES;

EID: 84917737216     PISSN: 14760584     EISSN: 17448395     Source Type: Journal    
DOI: 10.1586/14760584.2015.955478     Document Type: Review

References (96)

1. Centers for Disease Control and Prevention (CDC). Chikungunya fever diagnosed among international travelers-United States, 2005-2006. MMWR Morb Mortal Wkly Rep 55(38):1040-2
2. Milne-Price S, Miazgowicz KL, Munster VJ. The emergence of the Middle East Respiratory Syndrome coronavirus. Pathog Dis 2014. [Epub ahead of print
3. Zhang Y, MacArthur C, Mubila L, Baker S. Control of neglected tropical diseases needs a long-term commitment. BMC Med 2010; 8:67
4. Arce A, Estirado A, Ordobas M, et al. Re-emergence of leishmaniasis in Spain: community outbreak in Madrid, Spain, 2009 to 2012. Euro Surveill 2013;18(30): 20546
5. Montgomery SP, Starr MC, Cantey PT, et al. Neglected parasitic infections in the United States: chagas disease. Am J Trop Med Hyg 2014;90(5):814-18
6. Settembre EC, Dormitzer PR, Rappuoli R. Bringing influenza vaccines into the 21st century. Hum Vaccin Immunother 2013; 10:3
7. Fries LF, Smith GE, Glenn GM. A recombinant viruslike particle influenza A (H7N9) vaccine. N Engl J Med 2013; 369(26):2564-6
8. Zhang N, Jiang S, Du L. Current advancements and potential strategies in the development of MERS-CoV vaccines. Expert Rev Vaccines 2014. [Epub ahead of print
9. De Groot AS. How the SARS vaccine effort can learn from HIV-speeding towards the future, learning from the past. Vaccine 2003;21(27-30):4095-104
10. De Groot AS, Moise L, Liu R, et al. Cross-conservation of T-cell epitopes: Now even more relevant to (H7N9) influenza vaccine design. Hum Vaccin Immunother 2014;10(2):256-62
11. Hotez PJ, Dumonteil E, Heffernan MJ, Bottazzi ME. Innovation for the 'bottom 100 million': eliminating neglected tropical diseases in the Americas. Adv Exp Med Biol 2013;764:1-12
12. Bockarie MJ, Kelly-Hope LA, Rebollo M, Molyneux DH. Preventive chemotherapy as a strategy for elimination of neglected tropical parasitic diseases: endgame challenges. Philos Trans R Soc Lond B Biol Sci 2013;368(1623):20120144
13. Molyneux DH, Malecela MN. Neglected tropical diseases and the millennium development goals: why the "other diseases" matter: reality versus rhetoric. Parasit Vectors 2011;4:234
14. Webster JP, Molyneux DH, Hotez PJ, Fenwick A. The contribution of mass drug administration to global health: past, present and future. Philos Trans R Soc Lond B Biol Sci 2014;369(1645):20130434
15. Hotez PJ, Diemert D, Bacon KM, et al. The human hookworm vaccine. Vaccine 2013;31(Suppl 2):B227-32
16. Eisen JA, MacCallum CJ. Genomics of emerging infectious disease: a PLoS collection. PLoS Biol 2009;7(10):e1000224
17. Blattman JN, Sourdive DJ, Murali-Krishna K, et al. Evolution of the T-cell repertoire during primary, memory, and recall responses to viral infection. J Immunol 2000;165:6081-90
18. Harrer T, Harrer E, Kalams SA, et al. Cytotoxic T-lymphocytes in asymptomatic long term nonprogressing HIV-1 infection. Breadth and specificity of the response and relation to in vivo viral quasispecies in a person with prolonged infection and low viral load. J Immunol 1996;156(7):2612-23
19. Doolan DL, Hoffman SL, Southwood S, et al. Degenerate cytotoxic T-cell epitopes from P. falciparum restricted by multiple HLA-A and HLA-B supertype alleles. Immunity 1997;7(1):97-112
20. Gianfrani C, Oseroff C, Sidney J, et al. Human memory CTL response specific for influenza A virus is broad and multispecific. Hum Immunol 2000;61(5):438-52
21. Mok H, Lee S, Wright DW, Crowe JE Jr. Enhancement of the CD8+ T-cell response to a subdominant epitope of respiratory syncytial virus by deletion of an immunodominant epitope. Vaccine 2008; 26(37):4775-82
22. Gillespie GM, Wills MR, Appay V, et al. Functional heterogeneity and high frequencies of cytomegalovirus-specific CD8 (+) T lymphocytes in healthy seropositive donors. J Virol 2000;74(17):8140-50
23. De Groot AS, Berzofsky JA. From Genome to Vaccine - New Immunoinformatics tools for vaccine design. Methods 2004;34(4): 425-8
24. Moise L, Buller RM, Schriewer J, et al. VennVax, a DNA-prime, peptide-boost multi-T-cell epitope poxvirus vaccine, induces protective immunity against vaccinia infection by T cell response alone. Vaccine 2011;29(3):501-11
25. Moss SF, Moise L, Lee DS, et al. HelicoVax: epitope-based therapeutic H. pylori vaccination in a mouse model of gastric cancer. Vaccine 2011;29(11):2085-91
26. Gregory SH, Mott S, Phung J, et al. Epitope-based vaccination against pneumonic tularemia. Vaccine 2009;27(39): 5299-306
27. Petrovsky N, Brusic V. Bioinformatics for study of autoimmunity. Autoimmunity 2006;39:635-43
28. De Groot AS, Martin W. Reducing risk, improving outcomes: bioengineering less immunogenic protein therapeutics. Clin Immunol 2009;131(2):189-201
29. Wang P, Sidney J, Dow C, et al. A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol 2008;4(4):e1000048
30. Elliott SL, Suhrbier A, Miles JJ, et al. Phase I trial of a CD8+ T-cell peptide epitope-based vaccine for infectious mononucleosis. J Virol 2008;82(3):1448-57
31. Rappuoli R, Covacci A. Reverse vaccinology and genomics. Science 2003;302(5645):602
32. Pederson T. The immunome. Mol Immunol 1999;36(15-16):1127-8
33. De Groot AS, Martin W. From immunome to vaccine: epitope mapping and vaccine design tools. Novartis Found Symp 2003; 254(57-72):discussion 72-6, 98-101:250-2
34. Doytchinova IA, Taylor P, Flower DR. Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the Immunone. J Biomed Biotechnol 2003;2003(5):267-90
35. Plotkin SA. Vaccines: correlates of vaccine-induced immunity. Clin Infect Dis 2008;47(3):401-9
36. Yao B, Zheng D, Liang S, Zhang C. Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods. PLoS One 2013;8(4):e62249
37. Crotty S. Follicular helper CD4 T cells (TFH). Annu Rev Immunol 2011;29: 621-63
38. Koita OA, Dabitao D, Mahamadou I, et al. Confirmation of Immunogenic Consensus Sequence HIV-1 T-cell Epitopes in Bamako, Mali and Providence, Rhode Island. Hum Vaccin 2006;2(3):119-28
39. McMurry JA, Gregory SH, Moise L, et al. 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 2007;25(16): 3179-91
40. De Groot AS, Marcon L, Bishop EA, et al. HIV vaccine development by computer assisted design: the GAIA vaccine. Vaccine 2005;23(17-18):2136-48
41. De Groot AS, McMurry J, Marcon L, et al. Developing an epitope-driven tuberculosis (TB) vaccine. Vaccine 2005;23(17-18): 2121-31
42. Schanen BC, De Groot AS, Moise L, et al. Coupling sensitive in vitro and in silico techniques to assess cross-reactive CD4(+) T cells against the swine-origin H1N1 influenza virus. Vaccine 2011; 29(17):3299-309
43. Zhang S, Desrosiers J, Aponte-Pieras JR, et al. Human immune responses to H. pylori HLA class II epitopes identified by immunoinformatic methods. PLoS ONE 2014;9(4):e94974
44. Mishra S, Losikoff PT, Self AA, et al. Peptide-pulsed dendritic cells induce the hepatitis C viral epitope-specific responses of naïve human T cells. Vaccine 2014;32(26): 3285-92
45. De Groot AS, Ardito M, Moise L, et al. Immunogenic consensus sequence t helper epitopes for a pan-burkholderia biodefense vaccine. Immunome Res 2011;7(2):7
46. De Groot AS, Moise L, Martin W, and et al. Analysis of ChimeriVax Japanese Encephalitis (JE) virus sequence for T cell epitopes and comparison to circulating wild type JE Virus strains. Vaccine 2007;25(47): 8077-84
47. De Groot AS, Ardito M, McClaine E, et al. Immunoinformatic comparison of T-cell epitopes contained in novel swine-origin influenza A (H1N1) virus with epitopes in 2008-09 conventional influenza vaccine. Vaccine 2009;27(42):5740-7
48. Elfaki ME, Khalil EA, Degroot AS, et al. Immunogenicity and immune modulatory effects of in silico predicted L. donovani candidate peptide vaccines. Hum Vaccin Immunother 2012;8(12):1769-74
49. Gomez M, Johnson S, Gennaro ML. Identification of secreted proteins of Mycobacterium tuberculosis by a bioinformatic approach. Infect Immun 2000;68(4):2323-7
50. ExPASy bioinformatics resource portal. Available from: www.expasy.org
51. McMurry JA, Kimball S, Lee JH, et al. Epitope-driven TB vaccine development: a streamlined approach using immuno-informatics, ELISpot assays, and HLA transgenic mice. Curr Mol Med 2007; 7(4):351-68
52. De Groot AS. Immunomics: discovering new targets for vaccines and therapeutics. Drug Discov Today 2006;11(5-6):203-9
53. De Groot AS, Ardito M, Terry F, et al. Low immunogenicity predicted for emerging avian-origin H7N9: implication for influenza vaccine design. Hum Vaccin Immunother 2013;9(5):950-6
54. Despommier DD, Gwadz RW, Hotez PJ, Knirsch CA. Parasitic diseases. 5th edition. Apple Trees Productions, LLC; New York, NY, USA: 2005
55. Gnanasekar M, Rao KV, He YX, et al. Novel phage display-based subtractive screening to identify vaccine candidates of Brugia malayi. Infect Immun 2004;72(8): 4707-15
56. Hintz M, Schares G, Taubert A, et al. Juvenile female Litomosoides sigmodontis produce an excretory/secretory antigen (Juvp120) highly modified with dimethylaminoethanol. Parasitology 1998; 117(Pt 3):265-71
57. Bowen DG, Walker CM. Mutational escape from CD8+ T cell immunity: HCV evolution, from chimpanzees to man. J Exp Med 2005;201(11):1709-14
58. Bailey J, Blankson JN, Wind-Rotolo M, Siliciano RF. Mechanisms of HIV-1 escape from immune responses and antiretroviral drugs. Curr Opin Immunol 2004;16(4): 470-6
59. Falk K, Rotzschke O, Stevanovic S, et al. Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature 1991;351(6324):290-6
60. Rotzschke O, Falk K, Stevanovic S, et al. Exact prediction of natural T cell epitope. Eur J Immunol 1991;21(11):2891-4
61. Sette S, Sidney J. Nine major HLA Class I supertypes account for the vast preponderance of HLA-A and -B polymorphism. Immunogenetics 1999; 50(3-4):210-12
62. Southwood S, Sidney J, Kondo A, et al. Several common HLA-DR types share largely overlapping peptide binding repertoires. J Immunol 1998;160(7): 3363-73
63. Messitt TJ, Terry F, Moise L, et al. A comparison of two methods for T cell epitope mapping: "cell free" in vitro versus immunoinformatics. Immunome Res 2011; 7(2):6
64. Moutaftsi M, Peters B, Pasquetto V, et al. A consensus epitope prediction approach identifies the breadth of murine T(CD8+)- cell responses to vaccinia virus. Nat Biotechnol 2006;24(7):817-19
65. Moise L, De Groot AS. Putting immunoinformatics to the test. Nat Biotechnol 2006;24(7):791-2
66. Cecil DL, Holt GE, Park KH, et al. Elimination of IL-10-inducing T-helper epitopes from an IGFBP-2 vaccine ensures potent antitumor activity. Cancer Res 2014; 74(10):2710-18
67. Moise L, Gutierrez AH, Bailey-Kellogg C, et al. The two-faced T cell epitope: examining the host-microbe interface with JanusMatrix. Hum Vaccin Immunother. 2013;9(7):1577-86
68. Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol 1990;215(3):403-10
69. He L, De Groot AS, Gutierrez AH, et al. Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage. BMC Bioinf 2014;15(Suppl 4):S1
70. Su LF, Kidd BA, Han A, et al. Virus-specific CD4(+) memory-phenotype T Cells are abundant in unexposed adults. Immunity 2013;38(2):373-83
71. Chung H, Pamp SJ, Hill JA, et al. Gut immune maturation depends on colonization with a host-specific microbiota. Cell 2012;149(7):1578-93
72. Lee YK, Mazmanian SK. Has the microbiota played a critical role in the evolution of the adaptive immune system? Science 2010;330(6012):1768-73
73. Lathrop SK, Bloom SM, Rao SM, et al. Peripheral education of the immune system by colonic commensal microbiota. Nature 2011;478(7368):250-4
74. Saito R, Smoot ME, Ono K, et al. A travel guide to Cytoscape plugins. Nat Methods 2012;9(11):1069-76
75. Calvo-Calle JM, Strug I, Nastke MD, et al. Human CD4+ T cell epitopes from vaccinia virus induced by vaccination or infection. PLoS Pathog 2007;3(10):1511-29
76. Weber CA, Mehta PJ, Ardito M, et al. T cell epitope: Friend or Foe? Immunogenicity of biologics in context. In Series "Optimizing the Future for Biotechnology Therapies, the Key Role of Protein Engineering". Adv Drug Del Rev 2009;61(11):965-76
77. Sette A, Sidney J. HLA supertypes and supermotifs: a functional perspective on HLA polymorphism. Curr Opin Immunol 1998;10(4):478-82
78. De Groot AS, Bosma A, Chinai N, et al. From genome to vaccine: in silico predictions, ex vivo verification. Vaccine 2001;19(31):4385-95
79. Jin X, Roberts CG, Nixon DF, et al. Identification of subdominant cytotoxic T lymphocyte epitopes encoded by autologous HIV type 1 sequences, using dendritic cell stimulation and computer-driven algorithm. AIDS Res Hum Retroviruses 2000;16(1): 67-76
80. De Groot AS, Bishop E, Khan B, et al. Engineering immunogenic consensus T helper epitopes for a cross-clade HIV vaccine. Methods 2004;34(4):476-87
81. Koren E, De Groot AS, Jawa V, et al. Clinical validation of the "in silico" prediction of immunogenicity of a human recombinant therapeutic protein. Clin Immunol 2007;124(1):26-32
82. Cohen T, Moise L, Ardito M, et al. A method for individualizing the prediction of immunogenicity of protein vaccines and biologic therapeutics: individualized T cell epitope measure (iTEM). J Biomed Biotechnol 2010;2010(pii):961752
83. Thomson SA, Burrows SR, Misko IS, et al. Targeting a polyepitope protein incorporating multiple class II-restricted viral epitopes to the secretory/endocytic pathway facilitates immune recognition by CD4+ cytotoxic T lymphocytes: a novel approach to vaccine design. J Virol 1998; 72(3):2246-52
84. Rodriguez F, Whitton JL. Enhancing DNA immunization. Virology 2000;268(2): 233-8
85. An LL, Rodriguez F, Harkins S, et al. Vaccine 2000;18(20):2132-41
86. Velders MP, Weijzen S, Eiben GL, et al. Defined flanking spacers and enhanced proteolysis is essential for eradication of established tumors by an epitope string DNA vaccine. J Immunol 2001;166(9): 5366-73
87. Livingston BD, Newman M, Crimi C, et al. Optimization of epitope processing enhances immunogenicity of multiepitope DNA vaccines. Vaccine 2001;19(32): 4652-60
88. iVAX tool kit. Available from: www. immunome.org/ivax/ivax-tool-kit/
89. EpiVax. Available from: www.EpiVax.com
90. Yang ZY, Werner HC, Kong WP, et al. Evasion of antibody neutralization in emerging severe acute respiratory syndrome coronaviruses. Proc Natl Acad Sci USA 2005;102(3):797-801
91. Bethony JM, Cole RN, Guo X, et al. Petri W, Reed S, Valenzuela JG, Hotez PJ. Vaccines to combat the neglected tropical diseases. Immunol Rev 2011;239(1):237-70
92. Abi Abdallah DS, Pavinski Bitar A, Oliveira F, et al. A listeria-based vaccine that secretes the sand fly salivary protein LJM11 confers long-term protection against vector-transmitted Leishmania major. Infect Immun 2014. [Epub ahead of print
93. Oliveira F, de Carvalho AM, de Oliveira CI. Sand-Fly Saliva-Leishmania-Man: the trigger trio. Front Immunol 2013;4:375. eCollection
94. Kazimírová M, Stibrániová I. Tick salivary compounds: their role in modulation of host defences and pathogen transmission. Front Cell Infect Microbiol 2013;3:43
95. De Groot AS, Einck L, Moise L, et al. Making vaccines "on demand": a potential solution for emerging pathogens and biodefense? Hum Vaccin Immunother 2013;9(9):1877-84
96. Murray CJ, Vos T, Lozano R, et al. Disability-adjusted life years (DALYs) for 291 diseases and injuries in 21 regions, 1990-2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet 2012;380(9859):2197-223