Motif inference reveals optimal CTL epitopes presented by HLA class I alleles highly prevalent in Southern Africa

Journal of Immunology

Volumn 176, Issue 8, 2006, Pages 4699-4705

  Honeyborne, Isobella ^a   Rathod, Almas ^b   Buchli, Rico ^c   Ramduth, Dhanwanthie ^d   Moodley, Eshia ^d   Rathnavalu, Prinisha ^d   Chetty, Senica ^d   Day, Cheryl ^a,d   Brander, Christian ^b   Hildebrand, William ^e   Walker, Bruce D ^b,f   Kiepiela, Photini ^d   Goulder, Philip J R ^a,b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

^c Pure Protein LLC   (United States)

^d UNIVERSITY OF KWAZULU NATAL   (South Africa)

^e UNIVERSITY OF OKLAHOMA COLLEGE OF MEDICINE   (United States)

^f HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; GAMMA INTERFERON; HLA A ANTIGEN; HLA ANTIGEN CLASS 1; HLA B ANTIGEN; HLA C ANTIGEN;

ALLELE; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; CYTOTOXIC T LYMPHOCYTE; ENZYME LINKED IMMUNOSPOT ASSAY; EPIDEMIC; GENE FREQUENCY; HLA TYPING; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNE RESPONSE; PRIORITY JOURNAL; PROTEIN MOTIF; SOUTH AFRICA;

EID: 33645765507     PISSN: 00221767     EISSN: None     Source Type: Journal    
DOI: 10.4049/jimmunol.176.8.4699     Document Type: Article

References (29)

1. Nixon, D. F., A. R. Townsend, J. G. Elvin, C. R. Rizza, J. Gallwey, and A. J. McMichael. 1988. HIV-1 gag-specific cytotoxic T lymphocytes defined with recombinant vaccinia virus and synthetic peptides. Nature 336: 484-487.
2. Venet, A., and B. D. Walker. 1993. Cytotoxic T-cell epitopes in HIV/SIV infection. AIDS 7(Suppl. 1): S117-S126.
3. Nicole Frahm, P. G., and C. Brander. 2003. Broad HIV-1 specific CTL responses reveal extensive class I binding promiscuity of HIV-1 derived optimally, defines CTL epitopes. B. T. Korber, C. Brander, B. F. Haynes, R. Koup, J. P. Moore, B. D. Walker, and D. I. Watkins, eds. Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, NM. LA-UR 04-8162. HIV Molecular Immunology and HIV/SIV Vaccine Databases, pp. 3-24.
4. Kiepiela, P., A. J. Leslie, I. Honeyborne, D. Ramduth, C. Thobakgale, S. Chetty, P. Rathnavalu, C. Moore, K. J. Pfafferott, L. Hilton, et al. 2004. Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature 432: 769-775.
5. Addo, M. M., X. G. Yu, A. Rathod, D. Cohen, R. L. Eldridge, D. Strick, M. N. Johnston, C. Corcoran, A. G. Wurcel, C. A. Fitzpatrick, et al. 2003. Comprehensive epitope analysis of human immunodeficiency virus type 1 (HIV-1)-specific T-cell responses directed against the entire expressed HIV-1 genome demonstrate broadly directed responses, but no correlation to viral load. J. Virol. 77: 2081-2092.
6. Draenert, R., M. Altfeld, C. Brander, N. Basgoz, C. Corcoran, A. G. Wurcel, D. R. Stone, S. A. Kalams, A. Trocha, M. M. Addo, et al. 2003. Comparison of overlapping peptide sets for detection of antiviral CD8 and CD4 T cell responses. J. Immunol. Methods 275: 19-29.
7. Steven, G. E. P. P. Marsh, and L. D. Barber. 2000. The HLA Facts Book. Academic Press, San Diego.
8. Guo, H. C., D. R. Madden, M. L. Silver, T. S. Jardetzky, J. C. Gorga, J. L. Strominger, and D. C. Wiley. 1993. Comparison of the P2 specificity pocket in three human histocompatibility antigens: HLA-A*6801, HLA-A*0201, and HLA-B*2705. Proc. Natl. Acad. Sci. USA 90: 8053-8057.
9. Madden, D. R., J. C. Gorga, J. L. Strominger, and D. C. Wiley. 1992. The three-dimensional structure of HLA-B27 at 2.1 Å resolution suggests a general mechanism for tight peptide binding to MHC. Cell 70: 1035-1048.
10. Madden, D. R., D. N. Garboczi, and D. C. Wiley. 1993. The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2. Cell 75: 693-708.
11. Boisgerault, F., I. Khalil, V. Tieng, F. Connan, T. Tabary, J. H. Cohen, J. Choppin, D. Charron, and A. Toubert. 1996. Definition of the HLA-A29 peptide ligand motif allows prediction of potential T-cell epitopes from the retinal soluble antigen, a candidate autoantigen in birdshot retinopathy. Proc. Natl. Acad. Sci. USA 93: 3466-3470.
12. Goulder, P. J., M. M. Addo, M. A. Altfeld, E. S. Rosenberg, Y. Tang, U. Govender, N. Mngqundaniso, K. Annamalai, T. U. Vogel, M. Hammond, et al. 2001. Rapid definition of five novel HLA-A*3002-restricted human immunodeficiency virus-specific cytotoxic T-lymphocyte epitopes by ELISPOT and infracellular cytokine staining assays. J. Virol. 75: 1339-1347.
13. Altfeld, M. A., A. Trocha, R. L. Eldridge, E. S. Rosenberg, M. N. Phillips, M. M. Addo, R. P. Sekaly, S. A. Kalams, S. A. Burchett, K. McIntosh, et al. 2000. Identification of dominant optimal HLA-B60- and HLA-B61-restricted cytotoxic T-lymphocyte (CTL) epitopes: rapid characterization of CTL responses by enzyme-linked immunospot assay. J. Virol. 74: 8541-8549.
14. Parham, P., C. E. Lomen, D. A. Lawlor, J. P. Ways, N. Holmes, H. L. Coppin, R. D. Salter, A. M. Wan, and P. D. Ennis. 1988. Nature of polymorphism in HLA-A, -B, and -C molecules. Proc. Natl. Acad. Sci. USA 85: 4005-4009.
15. Maier, R., K. Falk, O. Rotzschke, B. Maier, V. Gnau, S. Stevanovic, G. Jung, H. G. Rammensee, and A. Meyerhans. 1994. Peptide motifs of HLA-A3, -A24, and -B7 molecules as determined by pool sequencing. Immunogenetics 40: 306-308.
16. Barber, L. D., B. Gillece-Castro, L. Percival, X. Li, C. Clayberger, and P. Parham. 1995. Overlap in the repertoires of peptides bound in vivo by a group of related class I HLA-B allotypes. Curr. Biol. 5: 179-190.
17. Huczko, E. L., W. M. Bodnar, D. Benjamin, K. Sakaguchi, N. Z. Zhu, J. Shabanowitz, R. A. Henderson, E. Appella, D. F. Hunt, and V. H. Engelhard. 1993. Characteristics of endogenous peptides eluted from the class I MHC molecule HLA-B7 determined by mass spectrometry and computer modeling. J. Immunol. 151: 2572-2587.
18. Vilches, C., L. Sanz, R. de Pablo, M. E. Moreno, S. Puente, and M. Kreisler. 1996. Molecular characterization of the new alleles HLA-B*8101 and B*4407. Tissue Antigens 47: 139-142.
19. Falk, K., O. Rotzschke, M. Takiguchi, V. Gnau, S. Stevanovic, G. Jung, and H. G. Rammensee. 1995. Peptide motifs of HLA-B38 and B39 molecules. Immunogenetics 41: 162-164.
20. Falk, K., O. Rotzschke, B. Grahovac, D. Schendel, S. Stevanovic, V. Gnau, G. Jung, J. L. Strominger, and H. G. Rammensee. 1993. Allele-specific peptide ligand motifs of HLA-C molecules. Proc. Natl. Acad. Sci. USA 90: 12005-12009.
21. Rickinson, A. B., and D. J. Moss. 1997. Human cytotoxic T lymphocyte responses to Epstein-Barr virus infection. Annu. Rev. Immunol. 15: 405-431.
22. Masemola, A. M., T. N. Mashishi, G. Khoury, H. Bredell, M. Paximadis, T. Mathebula, D. Barkhan, A. Puren, E. Vardas, M. Colvin, et al. 2004. Novel and promiscuous CTL epitopes in conserved regions of Gag targeted by individuals with early subtype C HIV type 1 infection from southern Africa. J. Immunol. 173: 4607-4617.
23. Wilson, C. C., S. A. Kalams, B. M. Wilkes, D. J. Ruhl, F. Gao, B. H. Hahn, I. C. Hanson, K. Luzuriaga, S. Wolinsky, R. Koup, et al. 1997. Overlapping epitopes in human immunodeficiency virus type 1 gp120 presented by HLA A, B, and C molecules: effects of viral variation on cytotoxic T-lymphocyte recognition. J. Virol. 71: 1256-1264.
24. Sidney, J., S. Southwood, and A. Sette. 2005. Classification of A1- and A24-supertype molecules by analysis of their MHC-peptide binding repertoires. Immunogenetics 57: 393-408.
25. Krausa, P., C. Munz, W. Keilholz, S. Stevanovic, E. Y. Jones, M. Browning, M. Bunce, H. G. Rammensee, and A. McMichael. 2000. Definition of peptide binding motifs amongst the HLA-A*30 allelic group. Tissue Antigens 56: 10-18.
26. Falk, K., O. Rotzschke, M. Takiguchi, B. Grahovac, V. Gnau, S. Stevanovic, G. Jung, and H. G. Rammensee. 1994. Peptide motifs of HLA-A1, -A11, -A31, and -A33 molecules. Immunogenetics 40: 238-241.
27. Lund, O., M. Nielsen, C. Kesmir, A. G. Petersen, C. Lundegaard, P. Worning, C. Sylvester-Hvid, K. Lamberth, G. Roder, S. Justesen, et al. 2004. Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics 55: 797-810.
28. Sette, A., and J. Sidney. 1999. Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism. Immunogenetics 50: 201-212.
29. Yusim, K. S. J., I. Honeyborne, C. Calef, P. J. Goulder, and B. T. Korber. 2004. Enhanced motif scan: a tool to scan for HLA anchor residues in proteins. B. T. Korber, C. Brander, B. F. Haynes, R. Koup, J. P. Moore, B. D. Walker, and D. I. Watkins, eds. Los Alamos National Laboratory, Theoretical and Biophysics, Los Alamos, NM. LA-UR 04-8162. Immunology and HIV/SIV Vaccine Databases, pp. 24-36.