In silico-accelerated identification of conserved and immunogenic variola/vaccinia T-cell epitopes

Vaccine

Volumn 27, Issue 46, 2009, Pages 6471-6479

  Moise, Leonard ^a,b   McMurry, Julie A ^a   Buus, Soren ^c   Frey, Sharon ^d   Martin, William D ^a   De Groot, Anne S ^a,b,e  

^a EpiVax Inc   (United States)

^b UNIVERSITY OF RHODE ISLAND   (United States)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

^d SAINT LOUIS UNIVERSITY   (United States)

^e BROWN UNIVERSITY   (United States)

Author keywords

Epitope mapping; Smallpox; T lymphocyte epitopes

Indexed keywords

GAMMA INTERFERON; HLA ANTIGEN CLASS 1; HLA ANTIGEN CLASS 2; SMALLPOX VACCINE;

ADULT; AMINO ACID SEQUENCE; ANTIGEN BINDING; ARTICLE; BIOINFORMATICS; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; COMPUTER MODEL; CONTROLLED STUDY; CROSS REACTION; ENZYME LINKED IMMUNOSPOT ASSAY; EPITOPE MAPPING; HUMAN; HUMAN CELL; HUMAN EXPERIMENT; IMMUNOGENICITY; NORMAL HUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PEPTIDE SYNTHESIS; PERIPHERAL BLOOD MONONUCLEAR CELL; PRIORITY JOURNAL; SMALLPOX; SMALLPOX VIRUS; VACCINATION; VACCINIA VIRUS; VIRUS GENOME;

ADULT; COMPUTATIONAL BIOLOGY; CROSS REACTIONS; EPITOPE MAPPING; EPITOPES, T-LYMPHOCYTE; GENES, MHC CLASS I; GENES, MHC CLASS II; GENOME, VIRAL; HUMANS; OPEN READING FRAMES; SMALLPOX VACCINE; T-LYMPHOCYTES; VACCINIA VIRUS; VARIOLA VIRUS; YOUNG ADULT;

EID: 70350072668     PISSN: 0264410X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.vaccine.2009.06.018     Document Type: Article

References (32)

1. Rosenthal S.R., Merchlinsky M., Kleppinger C., and Goldenthal K.L. Developing new smallpox vaccines. Emerg Infect Dis 7 November-December (6) (2001) 920-926
2. Kemper A.R., Davis M.M., and Freed G.L. Expected adverse events in a mass smallpox vaccination campaign. Eff Clin Pract 5 March-April (2) (2002) 84-90
3. Schafer J.R., Jesdale B.M., George J.A., Kouttab N.M., and De Groot A.S. Prediction of well-conserved HIV-1 ligands using a matrix-based algorithm, EpiMatrix. Vaccine 16 (1998) 1880-1884
4. De Groot A.S., Jesdale B.M., Szu E., and Schafer J.R. An interactive web site providing MHC ligand predictions: Application to HIV research. AIDS Res Hum Retroviruses 13 (1997) 539-541
5. De Groot A.S., Rayner J., and Martin W. Modeling the immunogenicity of the therapeutic proteins using T cell epitope mapping. In: Brown F., and Suis A.M. (Eds). Immunogenicity of therapeutic biological products. Developments in biologicals vol. 112 (2003), Karger, Basel 71-80
6. Sette A., and Sidney J. Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism. Immunogenetics 50 November (3-4) (1999) 201-212
7. Southwood S., Sidney J., Kondo A., del Guercio M.F., Appella E., Hoffman S., et al. Several common HLA-DR types share largely overlapping peptide binding repertoires. J Immunol 160 (1998) 3363-3373
8. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J Mol Biol 215 (1990) 403-410
9. Meister G.E., Roberts C.G., Berzofsky J.A., and De Groot A.S. Two novel T cell epitope prediction algorithms based on MHC-binding motifs; comparison of predicted and published epitopes from Mycobacterium tuberculosis and HIV protein sequences. Vaccine 13 (1995) 581-591
10. De Groot A.S., and Berzofsky J.A. From genome to vaccine-new immunoinformatics tools for vaccine design. Methods 34 (2004) 425-428
11. De Groot A.S., Marcon L., Bishop E.A., Rivera D., Kutzler M., Weiner D.B., et al. HIV vaccine development by computer assisted design: the GAIA vaccine. Vaccine 23 March (17-18) (2005) 2136-2148
12. Sylvester-Hvid C., Kristensen N., Blicher T., Ferre H., Lauemoller S.L., Wolf X.A., et al. Establishment of a quantitative ELISA capable of determining peptide-MHC class I interaction. Tissue Antigens 59 April (4) (2002) 251-258
13. Reijonen H., and Kwok W.W. Use of HLA class II tetramers in tracking antigen-specific T cells and mapping T-cell epitopes. Methods 29 March (3) (2003) 282-288
14. Assarsson E., Greenbaum J.A., Sundström M., Schaffer L., Hammond J.A., Pasquetto V., et al. Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. Proc Natl Acad Sci U S A 105 February (6) (2008) 2140-2145
15. Schmitt J.F., and Stunnenberg H.G. Sequence and transcriptional analysis of the vaccinia virus HindIII I fragment. J Virol 62 June (6) (1988) 1889-1897
16. Buller R.M., and Palumbo G.J. Poxvirus pathogenesis. Microbiol Rev 55 March (1) (1991) 80-122
17. Fulginiti V.A., Papier A., Lane J.M., Neff J.M., and Henderson D.A. Smallpox vaccination: a review, part II: Adverse events. Clin Infect Dis 37 (2003) 251-271
18. + T-cell response. Nat Rev Immunol 4 (2004) 595-602
19. + T cells and antiviral protection. J Immunol 175 (2005) 4677-4685
20. Edghill-Smith Y., Golding H., Manischewitz J., King L.R., Scott D., Bray M., et al. Smallpox vaccine-induced antibodies are necessary and sufficient for protection against monkeypox virus. Nat Med 11 (2005) 740-747
21. Jing L., Chong T.M., Byrd B., McClurkan C.L., Huang J., Story B.T., et al. Dominance and diversity in the primary human CD4 T cell response to replication-competent vaccinia virus. J Immunol 178 May (10) (2007) 6374-6386
22. Jing L., Davies D.H., Chong T.M., Chun S., McClurkan C.L., Huang J., et al. An extremely diverse CD4 response to vaccinia virus in humans is revealed by proteome-wide T-cell profiling. J Virol 82 July (14) (2008) 7120-7134
23. Ostrout N.D., McHugh M.M., Tisch D.J., Moormann A.M., Brusic V., and Kazura J.W. Long-term T cell memory to human leucocyte antigen-A2 supertype epitopes in humans vaccinated against smallpox. Clin Exp Immunol 149 August (2) (2007) 265-273
24. Oseroff C., Kos F., Bui H.H., Peters B., Pasquetto V., Glenn J., et al. HLA class I-restricted responses to vaccinia recognize a broad array of proteins mainly involved in virulence and viral gene regulation. Proc Natl Acad Sci U S A 102 September (39) (2005) 13980-13985
25. Drexler I., Staib C., Kastenmuller W., Stevanović S., Schmidt B., Lemonnier F.A., et al. Identification of vaccinia virus epitope-specific HLA-A*0201-restricted T cells and comparative analysis of smallpox vaccines. Proc Natl Acad Sci U S A 100 January (1) (2003) 217-222
26. Sidney J., Grey H.M., Kubo R.T., and Sette A. Practical, biochemical and evolutionary implications of the discovery of HLA class I supermotifs. Immunol Today 17 June (6) (1996) 261-266
27. De Groot A.S., Rivera D.S., McMurry J.A., Buus S., and Martin W. Identification of immunogenic HLA-B7 "Achilles' heel" epitopes within highly conserved regions of HIV. Vaccine 26 June (24) (2008) 3059-3071
28. Kastenmuller W., Gasteiger G., Gronau J.H., Baier R., Ljapoci R., Busch D.H., et al. Cross-competition of CD8+ T cells shapes the immunodominance hierarchy during boost vaccination. J Exp Med 204 September (9) (2007) 2187-2198
29. Ishioka G.Y., Fikes J., Hermanson G., Livingston B., Crimi C., Qin M.S., et al. Utilization of MHC class I transgenic mice for development of minigene DNA vaccines encoding multiple HLA-restricted CTL epitopes. J Immunol 162 (1999) 3915
30. Oukka M., Manuguerra J.C., Livaditis N., Tourdot S., Riche N., Vergnon I., et al. Protection against lethal viral infection by vaccination with nonimmunodominant peptides. J Immunol 157 (1996) 3039
31. Tourdot S., Oukka M., Manuguerra J.C., Magafa V., Vergnon I., Riche N., et al. Chimeric peptides:a new approach to enhancing the immunogenicity of peptides with low MHC class I affinity: application in antiviral vaccination. J Immunol 159 (1997) 2391
32. Moutaftsi M., Peters B., Pasquetto V., Tscharke D.C., Sidney J., Bui H.H., et al. A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus. Nat Biotechnol 24 July (7) (2006) 817-819