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. 1994 Oct 1;180(4):1283–1293. doi: 10.1084/jem.180.4.1283

Naturally processed viral peptides recognized by cytotoxic T lymphocytes on cells chronically infected by human immunodeficiency virus type 1

PMCID: PMC2191672  PMID: 7523570

Abstract

We have established long-term cultures of several cell lines stably and uniformly expressing human immunodeficiency virus type 1 (HIV-1) in order to (a) identify naturally processed HIV-1 peptides recognized by cytotoxic T lymphocytes (CTL) from HIV-1-seropositive individuals and (b) consider the hypothesis that naturally occurring epitope densities on HIV-infected cells may limit their lysis by CTL. Each of two A2- restricted CD8+ CTL specific for HIV-1 gag or reverse transcriptase (RT) recognized a single naturally processed HIV-1 peptide in trifluoroacetic acid (TFA) extracts of infected cells: gag 77-85 (SLYNTVATL) or RT 476-484 (ILKEPVHGV). Both processed peptides match the synthetic peptides that are optimally active in cytotoxicity assays and have the consensus motif described for A2-associated peptides. Their abundances were approximately 400 and approximately 12 molecules per infected Jurkat-A2 cell, respectively. Other synthetic HIV-1 peptides active at subnanomolar concentrations were not present in infected cells. Except for the antigen processing mutant line T2, HIV- infected HLA-A2+ cell lines were specifically lysed by both A2- restricted CTL, although infected Jurkat-A2 cells were lysed more poorly by RT-specific CTL than by gag-specific CTL, suggesting that low cell surface density of a natural peptide may limit the effectiveness of some HIV-specific CTL despite their vigorous activity against synthetic peptide-treated target cells.

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Selected References

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  1. Anderson K., Cresswell P., Gammon M., Hermes J., Williamson A., Zweerink H. Endogenously synthesized peptide with an endoplasmic reticulum signal sequence sensitizes antigen processing mutant cells to class I-restricted cell-mediated lysis. J Exp Med. 1991 Aug 1;174(2):489–492. doi: 10.1084/jem.174.2.489. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Baltimore D., Feinberg M. B. HIV revealed: toward a natural history of the infection. N Engl J Med. 1989 Dec 14;321(24):1673–1675. doi: 10.1056/NEJM198912143212409. [DOI] [PubMed] [Google Scholar]
  3. Bennink J. R., Yewdell J. W. Recombinant vaccinia viruses as vectors for studying T lymphocyte specificity and function. Curr Top Microbiol Immunol. 1990;163:153–184. doi: 10.1007/978-3-642-75605-4_6. [DOI] [PubMed] [Google Scholar]
  4. Berzofsky J. A., Pendleton C. D., Clerici M., Ahlers J., Lucey D. R., Putney S. D., Shearer G. M. Construction of peptides encompassing multideterminant clusters of human immunodeficiency virus envelope to induce in vitro T cell responses in mice and humans of multiple MHC types. J Clin Invest. 1991 Sep;88(3):876–884. doi: 10.1172/JCI115389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Carmichael A., Jin X., Sissons P., Borysiewicz L. Quantitative analysis of the human immunodeficiency virus type 1 (HIV-1)-specific cytotoxic T lymphocyte (CTL) response at different stages of HIV-1 infection: differential CTL responses to HIV-1 and Epstein-Barr virus in late disease. J Exp Med. 1993 Feb 1;177(2):249–256. doi: 10.1084/jem.177.2.249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cerundolo V., Alexander J., Anderson K., Lamb C., Cresswell P., McMichael A., Gotch F., Townsend A. Presentation of viral antigen controlled by a gene in the major histocompatibility complex. Nature. 1990 May 31;345(6274):449–452. doi: 10.1038/345449a0. [DOI] [PubMed] [Google Scholar]
  7. Chen Z. W., Shen L., Miller M. D., Ghim S. H., Hughes A. L., Letvin N. L. Cytotoxic T lymphocytes do not appear to select for mutations in an immunodominant epitope of simian immunodeficiency virus gag. J Immunol. 1992 Dec 15;149(12):4060–4066. [PubMed] [Google Scholar]
  8. Cheynier R., Langlade-Demoyen P., Marescot M. R., Blanche S., Blondin G., Wain-Hobson S., Griscelli C., Vilmer E., Plata F. Cytotoxic T lymphocyte responses in the peripheral blood of children born to human immunodeficiency virus-1-infected mothers. Eur J Immunol. 1992 Sep;22(9):2211–2217. doi: 10.1002/eji.1830220905. [DOI] [PubMed] [Google Scholar]
  9. Clerici M., Giorgi J. V., Chou C. C., Gudeman V. K., Zack J. A., Gupta P., Ho H. N., Nishanian P. G., Berzofsky J. A., Shearer G. M. Cell-mediated immune response to human immunodeficiency virus (HIV) type 1 in seronegative homosexual men with recent sexual exposure to HIV-1. J Infect Dis. 1992 Jun;165(6):1012–1019. doi: 10.1093/infdis/165.6.1012. [DOI] [PubMed] [Google Scholar]
  10. Culmann B., Gomard E., Kiény M. P., Guy B., Dreyfus F., Saimot A. G., Sereni D., Lévy J. P. An antigenic peptide of the HIV-1 NEF protein recognized by cytotoxic T lymphocytes of seropositive individuals in association with different HLA-B molecules. Eur J Immunol. 1989 Dec;19(12):2383–2386. doi: 10.1002/eji.1830191231. [DOI] [PubMed] [Google Scholar]
  11. Del Val M., Schlicht H. J., Ruppert T., Reddehase M. J., Koszinowski U. H. Efficient processing of an antigenic sequence for presentation by MHC class I molecules depends on its neighboring residues in the protein. Cell. 1991 Sep 20;66(6):1145–1153. doi: 10.1016/0092-8674(91)90037-y. [DOI] [PubMed] [Google Scholar]
  12. Falk K., Rötzschke O., Deres K., Metzger J., Jung G., Rammensee H. G. Identification of naturally processed viral nonapeptides allows their quantification in infected cells and suggests an allele-specific T cell epitope forecast. J Exp Med. 1991 Aug 1;174(2):425–434. doi: 10.1084/jem.174.2.425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Falk K., Rötzschke O., Stevanović S., Jung G., Rammensee H. G. Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature. 1991 May 23;351(6324):290–296. doi: 10.1038/351290a0. [DOI] [PubMed] [Google Scholar]
  14. Fisher A. G., Collalti E., Ratner L., Gallo R. C., Wong-Staal F. A molecular clone of HTLV-III with biological activity. Nature. 1985 Jul 18;316(6025):262–265. doi: 10.1038/316262a0. [DOI] [PubMed] [Google Scholar]
  15. Hammond S. A., Bollinger R. C., Tobery T. W., Silliciano R. F. Transporter-independent processing of HIV-1 envelope protein for recognition by CD8+ T cells. Nature. 1993 Jul 8;364(6433):158–161. doi: 10.1038/364158a0. [DOI] [PubMed] [Google Scholar]
  16. Hoffenbach A., Langlade-Demoyen P., Dadaglio G., Vilmer E., Michel F., Mayaud C., Autran B., Plata F. Unusually high frequencies of HIV-specific cytotoxic T lymphocytes in humans. J Immunol. 1989 Jan 15;142(2):452–462. [PubMed] [Google Scholar]
  17. Hosken N. A., Bevan M. J. Defective presentation of endogenous antigen by a cell line expressing class I molecules. Science. 1990 Apr 20;248(4953):367–370. doi: 10.1126/science.2326647. [DOI] [PubMed] [Google Scholar]
  18. Hosmalin A., Clerici M., Houghten R., Pendleton C. D., Flexner C., Lucey D. R., Moss B., Germain R. N., Shearer G. M., Berzofsky J. A. An epitope in human immunodeficiency virus 1 reverse transcriptase recognized by both mouse and human cytotoxic T lymphocytes. Proc Natl Acad Sci U S A. 1990 Mar;87(6):2344–2348. doi: 10.1073/pnas.87.6.2344. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Irwin M. J., Heath W. R., Sherman L. A. Species-restricted interactions between CD8 and the alpha 3 domain of class I influence the magnitude of the xenogeneic response. J Exp Med. 1989 Oct 1;170(4):1091–1101. doi: 10.1084/jem.170.4.1091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Jacks T., Power M. D., Masiarz F. R., Luciw P. A., Barr P. J., Varmus H. E. Characterization of ribosomal frameshifting in HIV-1 gag-pol expression. Nature. 1988 Jan 21;331(6153):280–283. doi: 10.1038/331280a0. [DOI] [PubMed] [Google Scholar]
  21. Johnson R. P., Trocha A., Buchanan T. M., Walker B. D. Identification of overlapping HLA class I-restricted cytotoxic T cell epitopes in a conserved region of the human immunodeficiency virus type 1 envelope glycoprotein: definition of minimum epitopes and analysis of the effects of sequence variation. J Exp Med. 1992 Apr 1;175(4):961–971. doi: 10.1084/jem.175.4.961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Johnson R. P., Trocha A., Yang L., Mazzara G. P., Panicali D. L., Buchanan T. M., Walker B. D. HIV-1 gag-specific cytotoxic T lymphocytes recognize multiple highly conserved epitopes. Fine specificity of the gag-specific response defined by using unstimulated peripheral blood mononuclear cells and cloned effector cells. J Immunol. 1991 Sep 1;147(5):1512–1521. [PubMed] [Google Scholar]
  23. Koenig S., Earl P., Powell D., Pantaleo G., Merli S., Moss B., Fauci A. S. Group-specific, major histocompatibility complex class I-restricted cytotoxic responses to human immunodeficiency virus 1 (HIV-1) envelope proteins by cloned peripheral blood T cells from an HIV-1-infected individual. Proc Natl Acad Sci U S A. 1988 Nov;85(22):8638–8642. doi: 10.1073/pnas.85.22.8638. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Koup R. A., Pikora C. A., Luzuriaga K., Brettler D. B., Day E. S., Mazzara G. P., Sullivan J. L. Limiting dilution analysis of cytotoxic T lymphocytes to human immunodeficiency virus gag antigens in infected persons: in vitro quantitation of effector cell populations with p17 and p24 specificities. J Exp Med. 1991 Dec 1;174(6):1593–1600. doi: 10.1084/jem.174.6.1593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Lifson J. D., Reyes G. R., McGrath M. S., Stein B. S., Engleman E. G. AIDS retrovirus induced cytopathology: giant cell formation and involvement of CD4 antigen. Science. 1986 May 30;232(4754):1123–1127. doi: 10.1126/science.3010463. [DOI] [PubMed] [Google Scholar]
  26. Mackewicz C. E., Ortega H. W., Levy J. A. CD8+ cell anti-HIV activity correlates with the clinical state of the infected individual. J Clin Invest. 1991 Apr;87(4):1462–1466. doi: 10.1172/JCI115153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Meyerhans A., Dadaglio G., Vartanian J. P., Langlade-Demoyen P., Frank R., Asjö B., Plata F., Wain-Hobson S. In vivo persistence of a HIV-1-encoded HLA-B27-restricted cytotoxic T lymphocyte epitope despite specific in vitro reactivity. Eur J Immunol. 1991 Oct;21(10):2637–2640. doi: 10.1002/eji.1830211051. [DOI] [PubMed] [Google Scholar]
  28. Nixon D. F., Broliden K., Ogg G., Broliden P. A. Cellular and humoral antigenic epitopes in HIV and SIV. Immunology. 1992 Aug;76(4):515–534. [PMC free article] [PubMed] [Google Scholar]
  29. Nixon D. F., Townsend A. R., Elvin J. G., Rizza C. R., Gallwey J., McMichael A. J. HIV-1 gag-specific cytotoxic T lymphocytes defined with recombinant vaccinia virus and synthetic peptides. Nature. 1988 Dec 1;336(6198):484–487. doi: 10.1038/336484a0. [DOI] [PubMed] [Google Scholar]
  30. Pamer E. G. Direct sequence identification and kinetic analysis of an MHC class I-restricted Listeria monocytogenes CTL epitope. J Immunol. 1994 Jan 15;152(2):686–694. [PubMed] [Google Scholar]
  31. Pantaleo G., Graziosi C., Fauci A. S. New concepts in the immunopathogenesis of human immunodeficiency virus infection. N Engl J Med. 1993 Feb 4;328(5):327–335. doi: 10.1056/NEJM199302043280508. [DOI] [PubMed] [Google Scholar]
  32. Phillips R. E., Rowland-Jones S., Nixon D. F., Gotch F. M., Edwards J. P., Ogunlesi A. O., Elvin J. G., Rothbard J. A., Bangham C. R., Rizza C. R. Human immunodeficiency virus genetic variation that can escape cytotoxic T cell recognition. Nature. 1991 Dec 12;354(6353):453–459. doi: 10.1038/354453a0. [DOI] [PubMed] [Google Scholar]
  33. Pircher H., Moskophidis D., Rohrer U., Bürki K., Hengartner H., Zinkernagel R. M. Viral escape by selection of cytotoxic T cell-resistant virus variants in vivo. Nature. 1990 Aug 16;346(6285):629–633. doi: 10.1038/346629a0. [DOI] [PubMed] [Google Scholar]
  34. Rahemtulla A., Fung-Leung W. P., Schilham M. W., Kündig T. M., Sambhara S. R., Narendran A., Arabian A., Wakeham A., Paige C. J., Zinkernagel R. M. Normal development and function of CD8+ cells but markedly decreased helper cell activity in mice lacking CD4. Nature. 1991 Sep 12;353(6340):180–184. doi: 10.1038/353180a0. [DOI] [PubMed] [Google Scholar]
  35. Rammensee H. G., Rötzschke O., Falk K. MHC class I-restricted antigen processing--lessons from natural ligands. Chem Immunol. 1993;57:113–133. doi: 10.1159/000319185. [DOI] [PubMed] [Google Scholar]
  36. Riddell S. R., Gilbert M. J., Greenberg P. D. CD8+ cytotoxic T cell therapy of cytomegalovirus and HIV infection. Curr Opin Immunol. 1993 Aug;5(4):484–491. doi: 10.1016/0952-7915(93)90027-p. [DOI] [PubMed] [Google Scholar]
  37. Riviere Y., Tanneau-Salvadori F., Regnault A., Lopez O., Sansonetti P., Guy B., Kieny M. P., Fournel J. J., Montagnier L. Human immunodeficiency virus-specific cytotoxic responses of seropositive individuals: distinct types of effector cells mediate killing of targets expressing gag and env proteins. J Virol. 1989 May;63(5):2270–2277. doi: 10.1128/jvi.63.5.2270-2277.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Rowland-Jones S. L., Nixon D. F., Aldhous M. C., Gotch F., Ariyoshi K., Hallam N., Kroll J. S., Froebel K., McMichael A. HIV-specific cytotoxic T-cell activity in an HIV-exposed but uninfected infant. Lancet. 1993 Apr 3;341(8849):860–861. doi: 10.1016/0140-6736(93)93063-7. [DOI] [PubMed] [Google Scholar]
  39. Rötzschke O., Falk K., Deres K., Schild H., Norda M., Metzger J., Jung G., Rammensee H. G. Isolation and analysis of naturally processed viral peptides as recognized by cytotoxic T cells. Nature. 1990 Nov 15;348(6298):252–254. doi: 10.1038/348252a0. [DOI] [PubMed] [Google Scholar]
  40. Rötzschke O., Falk K., Stevanović S., Jung G., Walden P., Rammensee H. G. Exact prediction of a natural T cell epitope. Eur J Immunol. 1991 Nov;21(11):2891–2894. doi: 10.1002/eji.1830211136. [DOI] [PubMed] [Google Scholar]
  41. Salter R. D., Cresswell P. Impaired assembly and transport of HLA-A and -B antigens in a mutant TxB cell hybrid. EMBO J. 1986 May;5(5):943–949. doi: 10.1002/j.1460-2075.1986.tb04307.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Townsend A., Bodmer H. Antigen recognition by class I-restricted T lymphocytes. Annu Rev Immunol. 1989;7:601–624. doi: 10.1146/annurev.iy.07.040189.003125. [DOI] [PubMed] [Google Scholar]
  43. Tsomides T. J., Eisen H. N. Identification of naturally occurring peptides associated with MHC molecules. Chem Immunol. 1993;57:166–196. [PubMed] [Google Scholar]
  44. Tsomides T. J. Sample preparation for HPLC by Centricon ultrafiltration. Biotechniques. 1993 Apr;14(4):656–659. [PubMed] [Google Scholar]
  45. Tsomides T. J., Walker B. D., Eisen H. N. An optimal viral peptide recognized by CD8+ T cells binds very tightly to the restricting class I major histocompatibility complex protein on intact cells but not to the purified class I protein. Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11276–11280. doi: 10.1073/pnas.88.24.11276. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Tsubota H., Lord C. I., Watkins D. I., Morimoto C., Letvin N. L. A cytotoxic T lymphocyte inhibits acquired immunodeficiency syndrome virus replication in peripheral blood lymphocytes. J Exp Med. 1989 Apr 1;169(4):1421–1434. doi: 10.1084/jem.169.4.1421. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Udaka K., Tsomides T. J., Eisen H. N. A naturally occurring peptide recognized by alloreactive CD8+ cytotoxic T lymphocytes in association with a class I MHC protein. Cell. 1992 Jun 12;69(6):989–998. doi: 10.1016/0092-8674(92)90617-l. [DOI] [PubMed] [Google Scholar]
  48. Udaka K., Tsomides T. J., Walden P., Fukusen N., Eisen H. N. A ubiquitous protein is the source of naturally occurring peptides that are recognized by a CD8+ T-cell clone. Proc Natl Acad Sci U S A. 1993 Dec 1;90(23):11272–11276. doi: 10.1073/pnas.90.23.11272. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Van Bleek G. M., Nathenson S. G. Isolation of an endogenously processed immunodominant viral peptide from the class I H-2Kb molecule. Nature. 1990 Nov 15;348(6298):213–216. doi: 10.1038/348213a0. [DOI] [PubMed] [Google Scholar]
  50. Walker B. D., Chakrabarti S., Moss B., Paradis T. J., Flynn T., Durno A. G., Blumberg R. S., Kaplan J. C., Hirsch M. S., Schooley R. T. HIV-specific cytotoxic T lymphocytes in seropositive individuals. Nature. 1987 Jul 23;328(6128):345–348. doi: 10.1038/328345a0. [DOI] [PubMed] [Google Scholar]
  51. Walker B. D., Flexner C., Birch-Limberger K., Fisher L., Paradis T. J., Aldovini A., Young R., Moss B., Schooley R. T. Long-term culture and fine specificity of human cytotoxic T-lymphocyte clones reactive with human immunodeficiency virus type 1. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9514–9518. doi: 10.1073/pnas.86.23.9514. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Wallny H. J., Deres K., Faath S., Jung G., Van Pel A., Boon T., Rammensee H. G. Identification and quantification of a naturally presented peptide as recognized by cytotoxic T lymphocytes specific for an immunogenic tumor variant. Int Immunol. 1992 Oct;4(10):1085–1090. doi: 10.1093/intimm/4.10.1085. [DOI] [PubMed] [Google Scholar]
  53. Wilson I. A., Cox N. J. Structural basis of immune recognition of influenza virus hemagglutinin. Annu Rev Immunol. 1990;8:737–771. doi: 10.1146/annurev.iy.08.040190.003513. [DOI] [PubMed] [Google Scholar]
  54. Zhou X., Glas R., Liu T., Ljunggren H. G., Jondal M. Antigen processing mutant T2 cells present viral antigen restricted through H-2Kb. Eur J Immunol. 1993 Aug;23(8):1802–1808. doi: 10.1002/eji.1830230811. [DOI] [PubMed] [Google Scholar]
  55. Zweerink H. J., Gammon M. C., Utz U., Sauma S. Y., Harrer T., Hawkins J. C., Johnson R. P., Sirotina A., Hermes J. D., Walker B. D. Presentation of endogenous peptides to MHC class I-restricted cytotoxic T lymphocytes in transport deletion mutant T2 cells. J Immunol. 1993 Mar 1;150(5):1763–1771. [PubMed] [Google Scholar]
  56. di Marzo Veronese F., Sarngadharan M. G., Rahman R., Markham P. D., Popovic M., Bodner A. J., Gallo R. C. Monoclonal antibodies specific for p24, the major core protein of human T-cell leukemia virus type III. Proc Natl Acad Sci U S A. 1985 Aug;82(15):5199–5202. doi: 10.1073/pnas.82.15.5199. [DOI] [PMC free article] [PubMed] [Google Scholar]

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