Development and validation of a fluorescence polarization-based competitive peptide-binding assay for HLA-A*0201 - A new tool for epitope discovery

Biochemistry

Volumn 44, Issue 37, 2005, Pages 12491-12507

  Buchli, Rico ^a,b   VanGundy, Rodney S ^a   Hickman Miller, Heather D ^b   Giberson, Christopher F ^a   Bardet, Wilfried ^b   Hildebrand, William H ^a,b  

^a Pure Protein LLC   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL ENGINEERING; DISEASES; FLUORESCENCE; IMMUNOLOGY; POLARIZATION; POLYPEPTIDES;

BIOCHEMICAL ASSAYS; EPITOPES; FLUORESCENCE POLARIZATION; PEPTIDE BINDING;

BIOASSAY;

HLA A ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1;

ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; EPITOPE MAPPING; EVALUATION; FLUORESCENCE POLARIZATION; HIGH THROUGHPUT SCREENING; HLA SYSTEM; HUMAN; HUMAN CELL; IC 50; IMMUNOASSAY; INFECTION PREVENTION; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; QUANTITATIVE ASSAY; STANDARDIZATION; VALIDATION PROCESS;

BINDING SITES; EPITOPES; FLUORESCEIN-5-ISOTHIOCYANATE; HEPATITIS B VIRUS; HIV-1; HLA-A ANTIGENS; HUMANS; PEPTIDES; RECOMBINANT PROTEINS; SPECTROMETRY, FLUORESCENCE;

EID: 24944541417     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050255v     Document Type: Article

References (133)

1. Byrne, J. A., and Oldstone, M. B. (1984) Biology of cloned cytotoxic T lymphocytes specific for lymphocytic choriomeningitis virus: Clearance of virus in vivo, J. Virol. 51, 682-686.
2. + T cells specific for a single nonamer epitope of Listeria monocytogenes are protective in vivo, J. Exp. Med. 175, 1531-1538.
3. Heslop, H. E., Ng, C. Y., Li, C., Smith, C. A., Loftin, S. K., Krance, R. A., Brenner, M. K., and Rooney, C. M. (1996) Long-term restoration of immunity against Epstein-Barr virus infection by adoptive transfer of gene-modified virus-specific T lymphocytes, Nat. Med. 2, 551-555.
4. Jamieson, B. D., Butler, L. D., and Ahmed, R. (1987) Effective clearance of a persistent viral infection requires cooperation between virus-specific Lyt2+ T cells and nonspecific bone marrow-derived cells. J. Virol. 61, 3930-3937.
5. Kulkarni, A. B., Collins, P. L., Bacik, I., Yewdell, J. W., Bennink. J. R., Crowe, J. E., Jr., and Murphy, B. R. (1995) Cytotoxic T cells specific for a single peptide on the M2 protein of respiratory syncytial virus are the sole mediators of resistance induced by immunization with M2 encoded by a recombinant vaccinia virus. J. Virol. 69. 1261-1264.
6. Lin, Y. L., and Askonas, B. A. (1981) Biological properties of an influenza A virus-specific killer T cell clone. Inhibition of virus replication in vivo and induction of delayed-type hypersensitivity reactions, J. Exp. Med. 154, 225-234.
7. McMichael, A. J., Gotch, F. M., Noble, G. R., and Beare, P. A. (1983) Cytotoxic T-cell immunity to influenza, N. Engl. J. Med. 309, 13-17.
8. Nayersina, R., Fowler, P., Guilhot, S., Missale, G., Cerny, A., Schlicht, H. J., Vitiello, A., Chesnut, R., Person, J. L., Redeker, A. G. et al. (1993) HLA A2 restricted cytotoxic T lymphocyte responses to multiple hepatitis B surface antigen epitopes during hepatitis B virus infection, J. Immunol. 150, 4659-4671.
9. Riddell, S. R., Watanabe, K. S., Goodrich, J. M., Li, C. R., Agha, M. E., and Greenberg, P. D. (1992) Restoration of viral immunity in immunodeficient humans by the adoptive transfer of T cell clones, Science 257, 238-241.
10. + lymphocytes, Science 283, 857-860.
11. Yap, K. L., Ada, G. L., and McKenzie, I. F. (1978) Transfer of specific cytotoxic T lymphocytes protects mice inoculated with influenza virus, Nature 273, 238-239.
12. Hill, A. V., Elvin, J., Willis, A. C., Aidoo, M., Allsopp, C. E., Gotch, F. M., Gao, X. M., Takiguchi, M., Greenwood, B. M., Townsend, A. R. et al. (1992) Molecular analysis of the association of HLA-B53 and resistance to severe malaria, Nature 360, 434-439.
13. Le, T. P., Church, L. W., Corradin, G., Hunter, R. L., Charoenvit, Y., Wang, R., de la Vega, P., Sacci, J., Ballou, W. R., Kolodny, N., Kitov, S., Glenn, G. M., Richards, R. L., Alving, C. R., and Hoffman, S. L. (1998) Immunogenicity of Plasmodium falciparum circumsporozoite protein multiple antigen peptide vaccine formulated with different adjuvants, Vaccine 16, 305-312.
14. Feltkamp, M. C., Vreugdenhil, G. R., Vierboom, M. P., Ras, E., van der Burg, S. H., ter Schegget, J., Melief, C. J., and Kast, W. M. (1995) Cytotoxic T lymphocytes raised against a subdominant epitope offered as a synthetic peptide eradicate human papillomavirus type 16-induced tumors, Eur. J. Immunol. 25, 2638-2642.
15. Iwasaki, A., and Barber, B. H. (1998) Induction by DNA immunization of a protective antitumor cytotoxic T lymphocyte response against a minimal-epitope-expressing tumor, Cancer Immunol. Immunother. 45, 273-279.
16. Kittlesen, D. J., Thompson, L. W., Gulden, P. H., Skipper, J. C., Colella, T. A., Shabanowitz, J., Hunt, D. F., Engelhard, V. H., Slingluff, C. L., Jr., and Shabanowitz, J. A. (1998) Human melanoma patients recognize an HLA-A1-restricted CTL epitope from tyrosinase containing two cysteine residues: Implications for tumor vaccine development, J. Immunol. 160, 2099-2106.
17. Mayordomo, J. I., Loftus, D. J., Sakamoto, H., De Cesare, C. M., Appasamy, P. M., Lotze, M. T., Storkus, W. J., Appella, E., and DeLeo, A. B. (1996) Therapy of murine tumors with p53 wild-type and mutant sequence peptide-based vaccines, J. Exp. Med. 183, 1357-1365.
18. Melief, C. J. (1992) Tumor eradication by adoptive transfer of cytotoxic T lymphocytes, Adv. Cancer Res. 58, 143-175.
19. Melief, C. J., Offringa, R., Toes, R. E., and Kast, W. M. (1996) Peptide-based cancer vaccines, Curr. Opin. Immunol. 8, 651-657.
20. Morgan, D. J., Kreuwel, H. T., Fleck, S., Levitsky, H. I. Pardoll, D. M., and Sherman, L. A. (1998) Activation of low avidity CTL specific for a self-epitope results in tumor rejection but not autoimmunity, J. Immunol. 160, 643-651.
21. Muul, L. M., Spiess, P. J., Director, E. P., and Rosenberg, S. A. (1987) Identification of specific cytolytic immune responses against autologous tumor in humans bearing malignant melanoma, J. Immunol. 138, 989-995.
22. Vierboom, M. P., Nijman, H. W., Offringa, R., van der Voort, E. I., van Hall, T., van den Broek, L., Fleuren, G. J., Kenemans, P., Kast, W. M., and Melief, C. J. (1997) Tumor eradication by wild-type p53-specific cytotoxic T lymphocytes, J. Exp. Med. 186, 695-704.
23. Vose, B. M., and Bonnard, G. D. (1982) Human tumour antigens defined by cytotoxicity and proliferative responses of cultured lymphoid cells, Nature 296, 359-361.
24. Donnelly, J. J., Ulmer, J. B., Hawe, L. A., Friedman, A., Shi, X. P., Leander, K. R., Shiver, J. W., Oliff, A. I., Martinez, D., Montgomery, D. et al. (1993) Targeted delivery of peptide epitopes to class I major histocompatibility molecules by a modified Pseudomonas exotoxin, Proc. Natl. Acad. Sci. U.S.A. 90, 3530-3534.
25. Goletz, T. J., Klimpel, K. R., Leppla, S. H., Keith, J. M., and Berzofsky, J. A. (1997) Delivery of antigens to the MHC class I pathway using bacterial toxins, Hum. Immunol. 54, 129-136.
26. Gooding, L. R., and O'Connell, K. A. (1983) Recognition by cytotoxic T lymphocytes of cells expressing fragments of the SV40 tumor antigen, J. Immunol. 131, 2580-2586.
27. Kim, D. T., Mitchell, D. J., Brockstedt, D. G., Fong, L., Nolan, G. P., Fathman, C. G., Engleman, E. G., and Rothbard, J. B. (1997) Introduction of soluble proteins into the MHC class I pathway by conjugation to an HIV tat peptide, J. Immunol. 159, 1666-1668.
28. Moore, M. W., Carbone, F. R., and Bevan, M. J. (1988) Introduction of soluble protein into the class I pathway of antigen processing and presentation, Cell 54, 777-785.
29. Yewdell, J. W., and Bennink, J. R. (1990) The binary logic of antigen processing and presentation to T cells, Cell 62, 203-206.
30. Cease, K. B., and Berzofsky, J. A. (1994) Toward a vaccine for AIDS: The emergence of immunobiology-based vaccine development, Annu. Rev. Immunol. 12, 923-989.
31. Celis, E., Tsai, V., Crimi, C., DeMars, R., Wentworth, P. A., Chesnut, R. W., Grey, H. M., Sette, A., and Serra, H. M. (1994) Induction of anti-tumor cytotoxic T lymphocytes in normal humans using primary cultures and synthetic peptide epitopes, Proc. Natl. Acad. Sci. U.S.A. 91, 2105-2109.
32. Cox, A. L., Skipper, J., Chen, Y., Henderson, R. A., Darrow, T. L., Shabanowitz, J., Engelhard, V. H., Hunt, D. F., and Slingluff, C. L., Jr. (1994) Identification of a peptide recognized by five melanoma-specific human cytotoxic T cell lines, Science 264, 716-719.
33. Kast, W. M., Roux, L., Curren, J., Blom, H. J., Voordouw, A. C., Meloen, R. H., Kolakofsky, D., and Melief, C. J. (1991) Protection against lethal Sendai virus infection by in vivo priming of virus-specific cytotoxic T lymphocytes with a free synthetic peptide, Proc. Natl. Acad. Sci. U.S.A. 88, 2283-2287.
34. Kast, W. M., Brandt, R. M., Sidney, J., Drijfhout, J. W., Kubo, R. T., Grey, H. M., Melief, C. J., and Sette, A. (1994) Role of HLA-A motifs in identification of potential CTL epitopes in human papillomavirus type 16 E6 and E7 proteins, J. Immunol. 152, 3904-3912.
35. Marchand, M., van Baren, N., Weynants, P., Brichard, V., Dreno, B., Tessier, M. H., Rankin, E., Parmiani, G., Arienti, F., Humblet, Y., Bourlond, A., Vanwijck, R., Lienard, D., Beauduin, M., Dietrich, P. Y., Russo, V., Kerger, J., Masucci, G., Jager, E., De Greve, J., Atzpodien, J., Brasseur, F., Coulie, P. G., van der Bruggen, P., and Boon, T. (1999) Tumor regressions observed in patients with metastatic melanoma treated with an antigenic peptide encoded by gene MAGE-3 and presented by HLA-A1, Int. J. Cancer 80, 219-230.
36. Oukka, M., Manuguerra, J. C., Livaditis, N., Tourdot, S., Riche, N., Vergnon, I., Cordopatis, P., and Kosmatopoulos, K. (1996) Protection against lethal viral infection by vaccination with nonimmunodominant peptides, J. Immunol. 157, 3039-3045.
37. Rosenberg, S. A., Yang, J. C., Schwartzentruber, D. J., Hwu, P., Marincola, F. M., Topalian, S. L., Restifo, N. P., Dudley, M. E., Schwarz, S. L., Spiess, P. J., Wunderlich, J. R., Parkhurst, M. R., Kawakami, Y., Seipp, C. A., Einhorn, J. H., and White, D. E. (1998) Immunologic and therapeutic evaluation of a synthetic peptide vaccine for the treatment of patients with metastatic melanoma, Nat. Med. 4, 321-327.
38. Schulz, M., Zinkernagel, R. M., and Hengartner, H. (1991) Peptide-induced antiviral protection by cytotoxic T cells, Proc. Natl. Acad. Sci. U.S.A. 88, 991-993.
39. An, L. L., and Whitton, J. L. (1997) A multivalent minigene vaccine, containing B-cell, cytotoxic T-lymphocyte, and Th epitopes from several microbes, induces appropriate responses in vivo and confers protection against more than one pathogen, J. Virol. 71, 2292-2302.
40. Ishioka, G. Y., Fikes, J., Hermanson, G., Livingston, B., Crimi, C., Qin, M., del Guercio, M. F., Oseroff, C., Dahlberg, C., Alexander, J., Chesnut, R. W., and Sette, A. (1999) Utilization of MHC class I transgenic mice for development of minigene DNA vaccines encoding multiple HLA-restricted CTL epitopes, J. Immunol. 162, 3915-3925.
41. Tourdot, S., Oukka, M., Manuguerra, J. C., Magafa, V., Vergnon, I., Riche, N., Bruley-Rosset, M., Cordopatis, P., and Kosmatopoulos, K. (1997) Chimeric peptides: A new approach to enhancing the immunogenicity of peptides with low MHC class I affinity: Application in antiviral vaccination, J. Immunol. 159, 2391-2398.
42. Disis, M. L., Gralow, J. R., Bernhard, H., Hand, S. L., Rubin, W. D., and Cheever, M. A. (1996) Peptide-based, but not whole protein, vaccines elicit immunity to HER-2/neu, oncogenic self-protein, J. Immunol. 156, 3151-3158.
43. Bjorkman, P. J., Saper, M. A., Samraoui, B., Bennett, W. S., Strominger, J. L., and Wiley, D. C. (1987) Structure of the human class I histocompatibility antigen, HLA-A2, Nature 329, 506-512.
44. Bjorkman, P. J., Saper, M. A., Samraoui, B., Bennett, W. S., Strominger, J. L., and Wiley, D. C. (1987) The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens, Nature 329, 512-518.
45. Rotzschke, O., Falk, K., Deres, K., Schild, H., Norda, M., Metzger, J., Jung, G., and Rammensee, H. G. (1990) Isolation and analysis of naturally processed viral peptides as recognized by cytotoxic T cells, Nature 348, 252-254.
46. Townsend, A. R., Rothbard, J., Gotch, F. M., Bahadur, G., Wraith, D., and McMichael, A. J. (1986) The epitopes of influenza nucleoprotein recognized by cytotoxic T lymphocytes can be defined with short synthetic peptides, Cell 44, 959-968.
47. van Bleek, G. M., and Nathenson, S. G. (1990) Isolation of an endogenously processed immunodominant viral peptide from the class I H-2Kb molecule, Nature 348, 213-216.
48. Sette, A., Vitiello, A., Reherman, B., Fowler, P., Nayersina, R., Kast, W. M., Melief, C. J., Oseroff, C., Yuan, L., Ruppert, J. et al. (1994) The relationship between class I binding affinity and immunogenicity of potential cytotoxic T cell epitopes, J. Immunol. 153, 5586-5592.
49. van der Burg, S. H., Visseren, M. J., Brandt, R. M., Kast, W. M., and Melief, C. J. (1996) Immunogenicity of peptides bound to MHC class I molecules depends on the MHC-peptide complex stability, J. Immunol. 156, 3308-3314.
50. Baker, B. M., Gagnon, S. J., Biddison, W. E., and Wiley, D. C. (2000) Conversion of a T cell antagonist into an agonist by repairing a defect in the TCR/peptide/MHC interface: Implications for TCR signaling, Immunity 13, 475-484.
51. Chen, W., Khilko, S., Fecondo, J., Margulies, D. H., and McCluskey, J. (1994) Determinant selection of major histocompatibility complex class I-restricted antigenic peptides is explained by class I-peptide affinity and is strongly influenced by nondominant anchor residues, J. Exp. Med. 180, 1471-1483.
52. Feltkamp, M. C., Vierboom, M. P., Kast, W. M., and Melief, C. J. (1994) Efficient MHC class I-peptide binding is required but does not ensure MHC class I-restricted immunogenicity, Mol. Immunol. 31, 1391-1401.
53. Kersh, G. J., Kersh, E. N., Fremont, D. H., and Allen, P. M. (1998) High- and low-potency ligands with similar affinities for the TCR: The importance of kinetics in TCR signaling, Immunity 9, 817-826.
54. Rammensee, H. G., Falk, K., and Rotzschke, O. (1993) Peptides naturally presented by MHC class I molecules, Annu. Rev. Immunol. 11, 213-244.
55. Ressing, M. E., Sette, A., Brandt, R. M., Ruppert, J., Wentworth, P. A., Hartman, M., Oseroff, C., Grey, H. M., Melief, C. J., and Kast, W. M. (1995) Human CTL epitopes encoded by human papillomavirus type 16 E6 and E7 identified through in vivo and in vitro immunogenicity studies of HLA-A*0201-binding peptides, J. Immunol. 154, 5934-5943.
56. Sette, A., Sidney, J., del Guercio, M. F., Southwood, S., Ruppert, J., Dahlberg, C., Grey, H. M., and Kubo, R. T. (1994) Peptide binding to the most frequent HLA-A class I alleles measured by quantitative molecular binding assays, Mol. Immunol. 31, 813-822.
57. Babbitt, B. P., Matsueda, G., Haber, E., Unanue, E. R., and Allen, P. M. (1986) Antigenic competition at the level of peptide-Ia binding, Proc. Natl. Acad. Sci. U.S.A. 83, 4509-4513.
58. Bouillot, M., Choppin, J., Cornille, F., Martinon, F., Papo, T., Gomard, E., Fournie-Zaluski, M. C., and Levy, J. P. (1989) Physical association between MHC class I molecules and immunogenic peptides, Nature 339, 473-475.
59. Werdelin, O. (1982) Chemically related antigens compete for presentation by accessory cells to T cells, J. Immunol. 129, 1883-1891.
60. Schumacher, T. N., Heemels, M. T., Neefjes, J. J., Kast, W. M., Melief, C. J., and Ploegh, H. L. (1990) Direct binding of peptide to empty MHC class I molecules on intact cells and in vitro, Cell 62, 563-567.
61. Hosken, N. A., and Bevan, M. J. (1990) Defective presentation of endogenous antigen by a cell line expressing class I molecules, Science 248, 367-370.
62. Townsend, A., Elliott, T., Cerundolo, V., Foster, L., Barber, B., and Tse, A. (1990) Assembly of MHC class I molecules analyzed in vitro, Cell 62, 285-295.
63. Luescher, I. F., Loez, J. A., Malissen, B., and Cerottini, J. C. (1992) Interaction of antigenic peptides with MHC class I molecules on living cells studied by photoaffmity labeling, J. Immunol. 148, 1003-1011.
64. Cerundolo, V., Alexander, J., Anderson, K., Lamb, C., Cresswell, P., McMichael, A., Gotch, F., and Townsend, A. (1990) Presentation of viral antigen controlled by a gene in the major histocompatibility complex, Nature 345, 449-452.
65. Storkus, W. J., Zeh, H. J., III, Salter, R. D., and Lotze, M. T. (1993) Identification of T-cell epitopes: Rapid isolation of class I-presented peptides from viable cells by mild acid elution, J. Immunother. 14, 94-103.
66. van der Burg, S. H., Ras, E., Drijfhout, J. W., Benckhuijsen, W. E., Bremers, A. J., Melief, C. J., and Kast, W. M. (1995) An HLA class I peptide-binding assay based on competition for binding to class I molecules on intact human B cells. Identification of conserved HIV-1 polymerase peptides binding to HLA-A*0301, Hum. Immunol. 44, 189-198.
67. Townsend, A., Ohlen, C., Bastin, J., Ljunggren, H. G., Foster, L., and Karre, K. (1989) Association of class I major histocompatibility heavy and light chains induced by viral peptides, Nature 340, 443-448.
68. Huczko, E. L., Bodnar, W. M., Benjamin, D., Sakaguchi, K., Zhu, N. Z., Shabanowitz, J., Henderson, R. A., Appella, E., Hunt, D. F., and Engelhard, V. H. (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.
69. Elvin, J., Potter, C., Elliott, T., Cerundolo, V., and Townsend, A. (1993) A method to quantify binding of unlabeled peptides to class I MHC molecules and detect their allele specificity, J. Immunol. Methods 158, 161-171.
70. Fahnestock, M. L., Tamir, I., Narhi, L., and Bjorkman, P. J. (1992) Thermal stability comparison of purified empty and peptide-filled forms of a class I MHC molecule, Science 258, 1658-1662.
71. Gnjatic, S., Bressac-de Paillerets, B., Guillet, J. G., and Choppin, J. (1995) Mapping and ranking of potential cytotoxic T epitopes in the p53 protein: Effect of mutations and polymorphism on peptide binding to purified and refolded HLA molecules, Eur. J. Immunol. 25, 1638-1642.
72. Bijlmakers, M. J., Neefjes, J. J., Wojcik-Jacobs, E. H., and Ploegh, H. L. (1993) The assembly of H2-Kb class I molecules translated in vitro requires oxidized glutathione and peptide, Eur. J. Immunol. 23, 1305-1313.
73. Parker, K. C., DiBrino, M., Hull, L., and Coligan, J. E. (1992) The β-microglobulin dissociation rate is an accurate measure of the stability of MHC class I heterotrimers and depends on which peptide is bound, J. Immunol. 149, 1896-1904.
74. Ottenhoff, T. H., Geluk, A., Toebes, M., Benckhuijsen, W. E., van Meijgaarden, K. E., and Drijfhout, J. W. (1997) A sensitive fluorometric assay for quantitatively measuring specific peptide binding to HLA class I and class II molecules, J. Immunol. Methods 200, 89-97.
75. Jensen, P. E., Moore, J. C., and Lukacher, A. E. (1998) A europium fluoroimmunoassay for measuring peptide binding to MHC class I molecules, J. Immunol. Methods 215, 71-80.
76. Sigal, L. J., Berens, S., and Wylie, D. (1994) A lactate dehydrogenase (LDH)-based immunoassay for detection of cell surface antigens and its application to the study of MHC class I-binding peptides, J. Immunol. Methods 177, 261-268.
77. Buus, S., Stryhn, A., Winther, K., Kirkby, N., and Pedersen, L. O. (1995) Receptor-ligand interactions measured by an improved spun column chromatography technique. A high efficiency and high throughput size separation method, Biochim. Biophys. Acta 1243, 453-460.
78. Chen, B. P., and Parham, P. (1989) Direct binding of influenza peptides to class I HLA molecules, Nature 337, 743-745.
79. Olsen, A. C., Pedersen, L. O., Hansen, A. S., Nissen, M. H., Olsen, M., Hansen, P. R., Holm, A., and Buus, S. (1994) A quantitative assay to measure the interaction between immunogenic peptides and purified class I major histocompatibility complex molecules, Eur J. Immunol. 24, 385-392.
80. Khilko, S. N., Corr, M., Boyd, L. F., Lees, A., Inman, J. K., and Margulies, D. H. (1993) Direct detection of major histocompatibility complex class I binding to antigenic peptides using surface plasmon resonance. Peptide immobilization and characterization of binding specificity, J. Biol. Chem. 268, 15425-15434.
81. Ruppert, J., Sidney, J., Celis, E., Kubo, R. T., Grey, H. M., and Sette, A. (1993) Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules, Cell 74, 929-937.
82. Kessler, J. H., Mommaas, B., Mutis, T., Huijbers, I., Vissers, D., Benckhuijsen, W. E., Schreuder, G. M., Offringa, R., Goulmy, E., Melief, C. J., van der Burg, S. H., and Drijfhout, J. W. (2003) Competition-based cellular peptide binding assays for 13 prevalent HLA class I alleles using fluorescein-labeled synthetic peptides, Hum. Immunol. 64, 245-255.
83. Buus, S., Sette, A., Colon, S. M., Jenis, D. M., and Grey, H. M. (1986) Isolation and characterization of antigen-Ia complexes involved in T cell recognition, Cell 47. 1071-1077.
84. Checovich, W. J., Bolger, R. E., and Burke, T. (1995) Fluorescence polarization-A new tool for cell and molecular biology, Nature 375, 254-256.
85. Jameson, D. M., and Seifried, S. E. (1999) Quantification of protein-protein interactions using fluorescence polarization, Methods 19, 222-233.
86. Buchli, R., VanGundy, R. S., Hickman-Miller, H. D., Giberson, C. F., Bardet, W., and Hildebrand, W. H. (2004) Real-time measurement of in vitro peptide binding to soluble HLA-A*0201 by fluorescence polarization, Biochemistry 43, 14852-14863.
87. Prilliman, K., Lindsey, M., Zuo, Y., Jackson, K. W., Zhang, Y., and Hildebrand, W. (1997) Large-scale production of class I bound peptides: Assigning a signature to HLA-B*1501, Immunogenetics 45, 379-385.
88. Robbins, P. A., Garboczi, D. N., and Strominger, J. L. (1995) HLA-A*0201 complexes with two 10-Mer peptides differing at the P2 anchor residue have distinct refolding kinetics, J. Immunol. 154, 703-709.
89. Parker, K. C., Bednarek, M. A., and Coligan, J. E. (1994) Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains, J. Immunol. 152, 163-175.
90. Jacobs, S., Chang, K. J., and Cuatrecasas, P. (1975) Estimation of hormone receptor affinity by competitive displacement of labeled ligand: Effect of concentration of receptor and of labeled ligand, Biochem. Biophys. Res. Commun. 66, 687-692.
91. Rodbard, D. (1973) Mathematics of hormone-receptor interaction. I. Basic principles, Adv. Exp. Med. Biol. 36, 289-326.
92. Cheng, Y. C., and Prusoff, W. H. (1974) A new rapid assay for measuring deoxycytidylate- and deoxythymidylate-kinase activities, Anal. Biochem. 60, 545-550.
93. Kubo, R. T., Sette, A., Grey, H. M., Appella, E., Sakaguchi, K., Zhu, N. Z., Arnott, D., Sherman, N., Shabanowitz, J., Michel, H. et al. (1994) Definition of specific peptide motifs for four major HLA-A alleles, J. Immunol. 152, 3913-3924.
94. del Guercio, M. F., Sidney, J., Hermanson, G., Perez, C., Grey, H. M., Kubo, R. T., and Sette, A. (1995) Binding of a peptide antigen to multiple HLA alleles allows definition of an A2-like supertype, J. Immunol. 154, 685-693.
95. Wentworth, P. A., Vitiello, A., Sidney, J., Keogh, E., Chesnut, R. W., Grey, H., and Sette, A. (1996) Differences and similarities in the A2.1-restricted cytotoxic T cell repertoire in humans and human leukocyte antigen-transgenic mice, Eur. J. Immunol. 26, 97-101.
96. Bertoletti, A., Costanzo, A., Chisari, F. V., Levrero, M., Artini, M., Sette, A., Penna, A., Giuberti, T., Fiaccadori, F., and Ferrari, C. (1994) Cytotoxic T lymphocyte response to a wild type hepatitis B virus epitope in patients chronically infected by variant viruses carrying substitutions within the epitope, J. Exp. Med. 180, 933-943.
97. Bertoni, R., Sidney, J., Fowler, P., Chesnut, R. W., Chisari, F. V., and Sette, A. (1997) Human histocompatibility leukocyte antigen-binding supermotifs predict broadly cross-reactive cytotoxic T lymphocyte responses in patients with acute hepatitis, J. Clin. Invest. 100, 503-513.
98. Keogh, E., Fikes, J., Southwood, S., Celis, E., Chesnut, R., and Sette, A. (2001) Identification of new epitopes from four different tumor-associated antigens; Recognition of naturally processed epitopes correlates with HLA-A*0201-binding affinity, J. Immunol. 167, 787-796.
99. Vitiello, A., Sette, A., Yuan, L., Farness, P., Southwood, S., Sidney, J., Chesnut, R. W., Grey, H. M., and Livingston, B. (1997) Comparison of cytotoxic T lymphocyte responses induced by peptide or DNA immunization: Implications on immunogenicity and immunodominance, Eur. J. Immunol. 27, 671-678.
100. Solache, A., Morgan, C. L., Dodi, A. I., Morte, C., Scott, I., Baboonian, C., Zal, B., Goldman, J., Grundy, J. E., and Madrigal, J. A. (1999) Identification of three HLA-A*0201-restricted cytotoxic T cell epitopes in the cytomegalovirus protein pp65 that are conserved between eight strains of the virus, J. Immunol. 163, 5512-5518.
101. Barnea, E., Beer, I., Patoka, R., Ziv, T., Kessler, O., Tzehoval, E., Eisenbach, L., Zavazava, N., and Admon, A. (2002) Analysis of endogenous peptides bound by soluble MHC class I molecules: A novel approach for identifying tumor-specific antigens, Eur. J. Immunol. 32, 213-222.
102. Sidney, J., del Guercio, M. F., Southwood, S., Engelhard, V. H., Appella, E., Rammensee, H. G., Falk, K., Rotzschke, O., Takiguchi, M., Kubo, R. T. et al. (1995) Several HLA alleles share overlapping peptide specificities, J. Immunol. 154, 247-259.
103. Smith, K. D., and Lutz, C. T. (1996) Peptide-dependent expression of HLA-B7 on antigen processing-deficient T2 cells, J. Immunol. 156, 3755-3764.
104. Maier, R., Falk, K., Rotzschke, O., Maier, B., Gnau, V., Stevanovic, S., Jung, G., Rammensee, H. G., and Meyerhans, A. (1994) Peptide motifs of HLA-A3, -A24, and -B7 molecules as determined by pool sequencing, Immunogenetics 40, 306-308.
105. Sidney, J., Southwood, S., del Guercio, M. F., Grey, H. M., Chesnut, R. W., Kubo, R. T., and Sette, A. (1996) Specificity and degeneracy in peptide binding to HLA-B7-like class I molecules, J. Immunol. 157, 3480-3490.
106. Aarnoudse, C. A., Kruse, M., Konopitzky, R., Brouwenstijn, N., and Schrier, P. I. (2002) TCR reconstitution in Jurkat reporter cells facilitates the identification of novel tumor antigens by cDNA expression cloning, Int. J. Cancer 99, 7-13.
107. Monji, M., Nakatsura, T., Senju, S., Yoshitake, Y., Sawatsubashi, M., Shinohara, M., Kageshita, T., Ono, T., Inokuchi, A., and Nishimura, Y. (2004) Identification of a novel human cancer/testis antigen, KM-HN-1, recognized by cellular and humoral immune responses, Clin. Cancer Res. 10, 6047-6057.
108. Rubio-Godoy, V., Dutoit, V., Zhao, Y., Simon, R., Guillaume, P., Houghten, R., Romero, P., Cerottini, J. C., Pinilla, C., and Valmori, D. (2002) Positional scanning-synthetic peptide library-based analysis of self- and pathogen-derived peptide cross-reactivity with tumor-reactive Melan-A-specific CTL, J. Immunol. 169, 5696-5707.
109. + cytolytic T-lymphocyte clone, Cancer Res. 62, 2058-2063.
110. Pinilla, C., Rubio-Godoy, V., Dutoit, V., Guillaume, P., Simon, R., Zhao, Y., Houghten, R. A., Cerottini, J. C., Romero, P., and Valmori, D. (2001) Combinatorial peptide libraries as an alternative approach to the identification of ligands for tumor-reactive cytolytic T lymphocytes, Cancer Res. 61, 5153-5160.
111. Prilliman, K. R., Lindsey, M., Jackson, K. W., Cole, J., Bonner, R., and Hildebrand, W. H. (1998) Complexity among constituents of the HLA-B*1501 peptide motif, Immunogenetics 48, 89-97.
112. Sudo, T., Kamikawaji, N., Kimura, A., Date, Y., Savoie, C. J., Nakashima, H., Furuichi, E., Kuhara, S., and Sasazuki, T. (1995) Differences in MHC class I self-peptide repertoires among HLA-A2 subtypes, J. Immunol. 155, 4749-4756.
113. Hickman, H. D., Luis, A. D., Bardet, W., Buchli, R., Battson, C. L., Shearer, M. H., Jackson, K. W., Kennedy, R. C., and Hildebrand, W. H. (2003) Cutting edge: Class I presentation of host peptides following HIV infection, J. Immunol. 171, 22-26.
114. Rammensee, H., Bachmann, J., Emmerich, N. P., Bachor, O. A., and Stevanovic, S. (1999) SYFPEITHI: Database for MHC ligands and peptide motifs, Immunogenetics 50, 213-219.
115. Reche, P. A., Glutting, J. P., and Reinherz, E. L. (2002) Prediction of MHC class I binding peptides using profile motifs, Hum. Immunol. 63, 701-709.
116. Barber, B. (1997) Introduction: Emerging vaccine strategies, Semin. Immunol. 9, 269-270.
117. 50) of an enzymatic reaction, Biochem. Pharmacol. 22, 3099-3108.
118. van Elsas, A., van der Burg, S. H., van der Minne, C. E., Borghi, M., Mourer, J. S., Melief, C. J., and Schrier, P. I. (1996) Peptide-pulsed dendritic cells induce tumoricidal cytotoxic T lymphocytes from healthy donors against stably HLA-A*0201-binding peptides from the Melan-A/MART-1 self-antigen, Eur. J. Immunol. 26, 1683-1689.
119. Vitiello, A., Ishioka, G., Grey, H. M., Rose, R., Farness, P., LaFond, R., Yuan, L., Chisari, F. V., Furze, J., Bartholomeuz, R. et al. (1995) Development of a lipopeptide-based therapeutic vaccine to treat chronic HBV infection. I. Induction of a primary cytotoxic T lymphocyte response in humans, J. Clin. Invest. 95, 341-349.
120. Goulder, P. J., Sewell, A. K., Lalloo, D. G., Price, D. A., Whelan, J. A., Evans, J., Taylor, G. P., Luzzi, G., Giangrande, P., Phillips, R. E., and McMichael, A. J. (1997) Patterns of immunodominance in HIV-1-specific cytotoxic T lymphocyte responses in two human histocompatibility leukocyte antigens (HLA)-identical siblings with HLA-A*0201 are influenced by epitope mutation, J. Exp. Med. 185, 1423-1433.
121. Goulder, P. J., Altfeld, M. A., Rosenberg, E. S., Nguyen, T., Tang, Y., Eldridge, R. L., Addo, M. M., He, S., Mukherjee, J. S., Phillips, M. N., Bunce, M., Kalams, S. A., Sekaly, R. P., Walker, B. D., and Brander, C. (2001) Substantial differences in specificity of HIV-specific cytotoxic T cells in acute and chronic HIV infection, J. Exp. Med. 193, 181-194.
122. Ogg, G. S., Jin, X., Bonhoeffer, S., Dunbar, P. R., Nowak, M. A., Monard, S., Segal, J. P., Cao, Y., Rowland-Jones, S. L., Cerundolo, V., Hurley, A., Markowitz, M., Ho, D. D., Nixon, D. F., and McMichael, A. J. (1998) Quantitation of HIV-1-specific cytotoxic T lymphocytes and plasma load of viral RNA, Science 279, 2103-2106.
123. Gotch, F., Rothbard, J., Howland, K., Townsend, A., and McMichael, A. (1987) Cytotoxic T lymphocytes recognize a fragment of influenza virus matrix protein in association with HLA-A2, Nature 326, 881-882.
124. Gotch, F., McMichael, A., Rothbard, J., McMichael, A. J., Gotch, F. M., Santos-Aguado, J., Strominger, J. L., Howland, K., and Townsend, A. (1988) Recognition of influenza A matrix protein by HLA-A2-restricted cytotoxic T lymphocytes. Use of analogues to orientate the matrix peptide in the HLA-A2 binding site, J. Exp. Med. 168, 2045-2057.
125. McMichael, A. J., Gotch, F. M., Santos-Aguado, J., and Strominger, J. L. (1988) Effect of mutations and variations of HLA-A2 on recognition of a virus peptide epitope by cytotoxic T lymphocytes, Proc. Natl. Acad. Sci. U.S.A. 85, 9194-9198.
126. Chen, B. P., Rothbard, J., and Parham, P. (1990) Apparent lack of MHC restriction in binding of class I HLA molecules to solid-phase peptides, J. Exp. Med. 172, 931-936.
127. Robbins, P. A., Lettice, L. A., Rota, P., Santos-Aguado, J., Rothbard, J., McMichael, A. J., Strominger, J. L., Burakoff, S. J., Vega, M. A., and Gotch, F. M. (1989) Comparison between two peptide epitopes presented to cytotoxic T lymphocytes by HLA-A2. Evidence for discrete locations within HLA-A2, J. Immunol. 143, 4098-4103.
128. Shimojo, N., Cowan, E. P., Engelhard, V. H., Maloy, W. L., Coligan, J. E., and Biddison, W. E. (1989) A single amino acid substitution in HLA-A2 can alter the selection of the cytotoxic T lymphocyte repertoire that responds to influenza virus matrix peptide 55-73, J. Immunol. 143, 558-564.
129. Gammon, M. C., Bednarek, M. A., Biddison, W. E., Bondy, S. S., Hermes, J. D., Mark, G. E., Williamson, A. R., and Zweerink, H. J. (1992) Endogenous loading of HLA-A2 molecules with an analog of the influenza virus matrix protein-derived peptide and its inhibition by an exogenous peptide antagonist, J. Immunol. 148, 7-12.
130. Vitiello, A., Marchesini, D., Furze, J., Sherman, L. A., and Chesnut, R. W. (1991) Analysis of the HLA-restricted influenza-specific cytotoxic T lymphocyte response in transgenic mice carrying a chimeric human-mouse class I major histocompatibility complex, J. Exp. Med. 173, 1007-1015.
131. Chen, Y., Sidney, J., Southwood, S., Cox, A. L., Sakaguchi, K., Henderson, R. A., Appella, E., Hunt, D. F., Sette, A., and Engelhard, V. H. (1994) Naturally processed peptides longer than nine amino acid residues bind to the class I MHC molecule HLA-A2.1 with high affinity and in different conformations, J. Immunol. 152, 2874-2881.
132. Man, S., Newberg, M. H., Crotzer, V. L., Luckey, C. J., Williams, N. S., Chen, Y., Huczko, E. L., Ridge, J. P., and Engelhard, V. H. (1995) Definition of a human T cell epitope from influenza A non-structural protein 1 using HLA-A2.1 transgenic mice, Int. Immunol. 7, 597-605.
133. Brander, C., Hartman, K. E., Trocha, A. K., Jones, N. G., Johnson, R. P., Korber, B., Wentworth, P., Buchbinder, S. P., Wolinsky, S., Walker, B. D., and Kalams, S. A. (1998) Lack of strong immune selection pressure by the immunodominant, HLA-A*0201-restricted cytotoxic T lymphocyte response in chronic human immunodeficiency virus-1 infection, J. Clin. Invest. 101, 2559-2566.