Recognition of HIV-1 peptides by host CTL is related to HIV-1 similarity to human proteins

PLoS ONE

Volumn 2, Issue 9, 2007, Pages

  Rolland, Morgane ^a   Nickle, David C ^a   Deng, Wenjie ^a   Frahm, Nicole ^b   Brander, Christian ^b   Learn, Gerald H ^a   Heckerman, David ^c   Jojic, Nebosja ^c   Jojic, Vladimir ^c   Walker, Bruce D ^b   Mullins, James I ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

^c MICROSOFT RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; HUMAN IMMUNODEFICIENCY VIRUS ANTIGEN; NEF PROTEIN; PROTEOME; VIRUS PROTEIN; PROTEIN;

AMINO ACID SEQUENCE; ANTIGEN RECOGNITION; ARTICLE; CONSENSUS SEQUENCE; CONTROLLED STUDY; CYTOTOXIC T LYMPHOCYTE; ENZYME LINKED IMMUNOSPOT ASSAY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNE RESPONSE; IMMUNOGENICITY; IMMUNOREACTIVITY; MAJOR CLINICAL STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEOMICS; SEQUENCE HOMOLOGY; CHEMISTRY; ENZYME LINKED IMMUNOSORBENT ASSAY; IMMUNOLOGY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

AMINO ACID SEQUENCE; ENZYME-LINKED IMMUNOSORBENT ASSAY; GENE PRODUCTS, NEF; HIV-1; HUMANS; PROTEINS; PROTEOME; SEQUENCE HOMOLOGY, AMINO ACID; T-LYMPHOCYTES, CYTOTOXIC;

EID: 41049100092     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000823     Document Type: Article

References (58)

1. Borrow P, Lewick H, Hahn BH, Shaw GM, Oldstone MBA (1994) Virus-specific CD8+ cytoxic T-lymphocyte activity associated with control of viremia in primary HIV-1 infection. J Virol 68: 6103-6110.
2. Klein MvB, CA Holwerda AM, et al. (1995) Kinetics of gag-specific cytotoxic T lymphocyte responses during the clinical course of HIV-1 infection: A longitudinal analysis of rapid progressors and long-term asymptomatics. J Exp Med 181: 1365-1372.
3. Musey L, Hughes J, Schacker T, Shea T, Corey L, et al. (1997) Envelope cytotoxic T cell responses correlate with viral load and disease progression in early HIV-1 infection. N Engl J Med 337: 1267-1274.
4. Metzner KJ, Jin X, Lee FV, Gettie A, Bauer DE, et al. (2000) Effects of in vivo CD8(+) T cell depletion on virus replication in rhesus macaques immunized with a live, attenuated simian immunodeficiency virus vaccine. J Exp, Med 191: 1921-1931.
5. Letvin NL, Schmitz JE, Jordan HL, Seth A, Hirsch VM, et al. (1999) Cytotoxic T lymphocytes specific for the simian immunodeficiency virus. Inummol Rev 170: 127-134.
6. Schmitz JE, Kuroda MJ, Santra S, Sasseville VG, Simon MA, et al. (1999) Control of viremia in simian immunodeficiency virus infection by CD8+ lymphocytes. Science 283: 857-860.
7. Yewdell JW, Bermink JR (1999) Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses. Annu Rev Immunol 17: 51-88.
8. Chen W, Anton LC, Bennink JR, Yewdell JW (2000) Dissecting the multifactorial causes of immunodominance in class I-restricted T cell responses to viruses. Immunity 12: 83-93.
9. Lichterfeld M, Yu XG, I.& Gall S, Altfeld M (2005) Immunodominance of HIV-1-specific CDB(+) T-cell responses in acute HIV-1 infection: at the crossroads of viral and host. genetics. Trends Immunol 26: 166-171.
10. Meyer-Olson D, Brady KW, Bartman MT, O'Sullivan KM, Simons BC, et al. (2006) Fluctuations of functionally distinct CD8+ T-cell clonotypes demonstrate flexibility of the HIV-specific TCR repertoire. Blood 107: 2373-2383.
11. Bihl F, Frahm N, Di Giammarino L, Sidney J, John M, et al. (2006) Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responses. J Immunol 176: 4094-4101.
12. Frahm N, Kerber BT, Adams CM, Szinger JJ, Draenert R, et al. (2004) Consistent cytotoxic-T-lymphocyte targeting of immunodominant regions in human immunodeficiency virus across multiple ethnicities. J Virol 78: 2187 2200.
13. Frahm N, Kiepiela P, Adams S, Linde CH, Hewitt HS, et al. (2006) Control of human immunodeficiency virus replication by cytotoxic T lymphocytes targeting subdominant epitopes. Nat Immunol 7: 173-178.
14. Jones NA, Wei Y, Flower DR, Wong M, Michor F, et al. (2004) Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response. J Exp Med 200: 1243-1256.
15. Lanzavecchia A (1995) How can cryptic epitopes trigger autoinimunity? J Exp Med 181: 1945-1948.
16. Moudgil KD, Sercars EE (2005) Understanding crypticity is the key to revealing the pathogenesis of autoinummity. Trends Immunol 26: 355-359.
17. Zhu H, Liu K, Cerny J, Imoto T, Moudgil KD (2005) Insertion of the dibasic, motif in the flanking region of a cryptic self-determinant leads to activation of the epitope-specific T cells. J Immunol 175: 2252-2260.
18. Jiang X, Moudgil KD (2006) The unveiling of hidden T-cell determinants of a native antigen by defined mediators of inflammation: implications for die pathogenesis of autoinimunity. Scand J Immunol 63: 338-346.
19. Reiher WEI, Blalock JE, Brunck TK (1986) Sequence homology between acquired immunodeficiency syndrome virus envelope protein and interleukin 2 (Correction, vol 84, p 564). ProcNatlAcadSciUSA 83: 9188-9192.
20. Lopalco L, De Santis C, Meneveri R, Longhi R, Ginelli E, et al. (1993) Human immunodeficiency virus type 1 gp 120 C5 region mimics the HIA class I alpha 1 peptide-biitding domain. Eur J Immunol 23: 2016-2021.
21. Cordiali P, Balzarotti V, Morante S, Parisi V, Pugliese O, et al. (1992) Convergent evolution in the homology between HIV gp160 and HIA class II molecules. AIDS Res Hum Retroviruses 8: 1561-1565.
22. Albini A, Ferrini S,Benelli R, Sforzini S, Giunciuglio D, et al. (1998) HIV-1 Tat protein mimicry of chemokines. Proc Natl Acad Sci U S A 95: 13153-13158.
23. Murphy PM (2001) Viral exploitation and subversion of the immune system through chemokine mimicry. Nat Immunol 2: 116-122.
24. Golding H,, Robey FA, Gates FT, Linder W, Beining PR, et al. (1988) Identification of homologous regions in human immunodeficiency virus I gp41 and human MHC class II beta 1 domain. I. Monoclonal antibodies against the gp41 -derived peptide and patients' sera react with native HLA class II antigens, suggesting A role for autoimmunity in the pathogenesis of acquired immune deficiency syndrome. JExpMed 167: 914-923.
25. Golding H, Shearer GM, Hillman K, Lucas P, Manischewitz J, et al. (1989) Common epitope in human immunodeficiency virus (HIV) I-GP41 and HLA class II elicits immunosuppressive autoantibodies capable of contributing to immune dysfunction in HIV I-infected individuals. JClinInvest 83: 1430-1435.
26. Habeshaw J, Hounsell E, Dalgleish A (1992) Does the HIV envelope induce a chronic graft-versus-host-like disease? Immunol Today 13: 207-210.
27. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
28. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
29. Deng W, Nickle DC, Learn GH, Maust B, Mullins JI ViroBLAST. A BLAST for flexible queries of multiple databases. Submitted.
30. Maksyutov AZ, Bachinskii AG, Bazhan SI, Ryzhikov EA, Maksyutov ZA (2004) Exclusion of HIV epitopes shared with human proteins is prerequisite for designing safer AIDS vaccines. J Clin Virol 31 Suppl 1:,S26-38.
31. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
32. McClure MA, Richardson HS, Clinton RA, Hepp CM, Crowther BA, et al. (2005) Automated characterization of potentially active retroid agents in the human genome. Genomics 85: 512-523.
33. Plotz PH (2003) The autoantibody repertoire: searching for order. Nat Rev Immunol 3: 73-78.
34. Inohara, Chamaillard, McDonald C, Nunez G (2005) NOD-LRR proteins: role in host-microbial interactions and inflammatory disease. Annu Rev Biochem 74:355-383.
35. Ting JP, Kastrier DL, Heffman HM (2006) CATERPILLERs, pyrin and hereditary immunological disorders. Nat Rev Immunol 6: 183-195.
36. Quan V, Towey M, Sacks S, Kelly AP (1999) Absence of MHC class 7 gene expression in a patient with a single amino acid substitution in the class II transactivator protein CIITA. Immunogenetics 49: 957 963.
37. Rakowiez-Szulczynska EM, Jackson B, Snyder W (1998) Prostate, breast and gynecological cancer markers RAK with homology to HIV-1. Cancer Lett 124: 213-223.
38. Yusim K, Kesmir C, Gaschen B, Addo MM, Weltfeld M, et al. (2002) Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion or HIV-1 global variation. J Virol 76: 8757-8768.
39. Lucchiari-Hartz M, Lindo V, Hitziger N, Gaedicke S, Saveanu L, et al. (2003) Differential proteasomal processing of hydrophobic and hydrophilic protein regions: Contribution to cytotoxic T lymphocyte epitope clustering in HIV-1- Nef. Proc Natl Acad Sci U S A 100: 7755-7760.
40. Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, et al. (2001) Intrinsically disordered protein. J Viol Graph Model 19: 26-59.
41. Dohlman JG, Lupas A, Carson M (1993) Long charge-rich alpha-helices in systemic autoantigens. Biochem Biophys Res Commun 195: 686-696.
42. Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337: 635-645.
43. Shojania S, O'Neil JD (2006) HIV-1 Tat is a natively unfolded proteir: the solution conformation and dynamics of reduced HIV-1 Tat-(1-72) by NMR spectroscopy. J Biol Chem 281: 8347-8356.
44. Goulder PJ, Sewell AK, Lalloo DG, Price DA, Whelan JA, et aL (1997) Patterns of immunodominance in HIV-1-specific cytotoxic T lymphocyte responses in two human histocompatibility leukocyte antigens (HLA)-identical siblings with HIA-A*0201 are influenced by epitope mutation. J Exp Med 185: 1423-1433.
45. Goulder PJ, Brander C, Annamalai Y, Mngqundaniso N, Govender U, et al. (2000) Differential narrow focusing of immunodominant human immunodeficiency virus gag-specific cytotoxic T-lymphocyte responses in infected African and caucasoid adults and childred. J Virol 74: 5679-5690.
46. Novitsky V, Cao H, Rybak N, Gilbert P, McLane MF, et al. (2002) Magnitude and frequency of cytotoxic T-lymphocyte responses: identification of immunodominant regions of human immunodeficiency virus type I subtype C. J Virol 76: 10155-10148.
47. Masemola A, Mashishi T, Khoury G, Mohube P, Mokgotho P, et al. (2004) Hierarchical targeting of subtype C human immunodeficiency virus type I proteins by CD8+ T cells: correlation with viral load. J Virol 78: 3233-3243.
48. Zuniga R, Lucchetti A, Galvan P, Sanchez S, Sanchez C, et al. (2006) Relative dominance of Gag p24-specific cytotoxic T lymphocytes is associated with human immunodefiency virus control. J Virol 780: 3122-3125.
49. Bonnet F, Pineau JJ, Taupin, JL, Feyler, A, Bonarek M, et al. (2003) Prevalence of cryoglobulinemia and serological markers of autoimmunity in human immuno-deficiency virus infected individuals: a cross-sectional study of 97 patients. J Rheumatol 30: 2005-2010.
50. Chretien P, Monier JC, Oksman, F, San, Marco M, Escande A, et al, (2003) Autoantibodies and human immunodeficiency virus infection: a case-control study. Clin Exp Rheumatol 21: 210-212:
51. De Keyser F; Hoch SO, Takei M, Dang H, De Keyser H, et al. (1992) Cross-reactivity of the B/B' subunit of the SM ribonucleoprotein autoantigen with proline-rich polypeptidcs. Clin Immunol Immunopathol 62: 285-290.
52. Gonzalez-Conejero R, Rivera J, Rosillo MC, Cano A, Rodriguez T, et al. (1996) Association of autoantibodies against platelet glycoprotein. Ib IX and IIb/IIIa, and platelet-reactive anti-HIV antibodies in thrombocytopenic narcotic addicts. Br J Haematol 93: 464-471
53. Haynes BF, Fleming J, St Clair EW, Katinger H, Stiegler G, et al. (2005) Cardiolipin polyspecific autoreactivity in two broadly neutralizing HIV-1 antibodies. Science 308: 1906-1998.
54. Talal N, Dauphinee MJ, Dang H, Alexander SS, Hart DJ, et al. (1990) Detection of serum antibodies to retroviral proteins in patients with primary Sjogren's syndrome (autoimmune exocrinopathy). Arthritis Rheum 33: 774-781.
55. Dyson HJ, Wright PE (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6: 197-208.
56. Berzofsky JA, Cease KB, Cornette JL, Spouge JL, Margalit H, et al. (1987) Protein antigenic structures recognized by T cells: potential applications to vaccine design. Immunol Rev 98: 9-52.
57. Obradovic Z, Peng K, Vucetic S, Radivojac P, Dunker AK (2005) Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins 61 Suppl 7: 176-182.
58. Jin Y, Dunbrack RL Jr (2005) Assessment of disorder predictions in CASP6. Proteins 61 Suppl 7: 167-175.