Resistance-associated epitopes of HIV-1C - Highly probable candidates for a multi-epitope vaccine

Immunogenetics

Volumn 64, Issue 10, 2012, Pages 767-772

  Sundaramurthi, Jagadish Chandrabose ^a   Swaminathan, Soumya ^a   Hanna, Luke Elizabeth ^a  

^a NATIONAL INSTITUTE FOR RESEARCH IN TUBERCULOSIS   (India)

Author keywords

Epitopes; HIV; HLA; Immune response; Molecular modeling; Vaccine

Indexed keywords

EPITOPE; HLA B ANTIGEN; HUMAN IMMUNODEFICIENCY VIRUS VACCINE;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; ALLELE; ARTICLE; CYTOTOXIC T LYMPHOCYTE; DISEASE COURSE; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1C; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNE RESPONSE; IMMUNOGENETICS; NONHUMAN; PRIORITY JOURNAL;

ACQUIRED IMMUNODEFICIENCY SYNDROME; AIDS VACCINES; EPITOPE MAPPING; EPITOPES, T-LYMPHOCYTE; HIV INFECTIONS; HIV-1; HLA ANTIGENS; HUMANS; IMMUNITY, CELLULAR; PEPTIDE FRAGMENTS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84866738142     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-012-0635-z     Document Type: Article

References (51)

1. Adar Y, Singer Y, Levi R, Tzehoval E, Perk S, Banet-Noach C, Nagar S, Arnon R, Ben-Yedidia T (2009) A universal epitope-based influenza vaccine and its efficacy against H5N1. Vaccine 27:2099-2107
2. Altfeld M, Kalife ET, Qi Y, Streeck H, Lichterfeld M, Johnston MN, Burgett N, Swartz ME, Yang A, Alter G, Yu XG, Meier A, Rockstroh JK, Allen TM, Jessen H, Rosenberg ES, Carrington M, Walker BD (2006) HLA alleles associated with delayed progression to AIDS contribute strongly to the initial CD8 (+) T cell response against HIV-1. PLoS Med 3:e403
3. Barouch DH (2008) Challenges in the development of an HIV-1 vaccine. Nature 455:613-619
4. Bihl F, Frahm N, Di Giammarino L, Sidney J, John M, Yusim K, Woodberry T, Sango K, Hewitt HS, Henry L, Linde CH, Chisholm JV 3rd, Zaman TM, Pae E, Mallal S, Walker BD, Sette A, Korber BT, Heckerman D, Brander C (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
5. Blackwell JM, Jamieson SE, Burgner D (2009) HLA and infectious diseases. Clin Microbiol Rev 22:370-385
6. Borbulevych OY, Baxter TK, Yu Z, Restifo NP, Baker BM (2005) Increased immunogenicity of an anchor-modified tumor-associated antigen is due to the enhanced stability of the pep-tide/MHC complex: implications for vaccine design. J Immunol 174:4812-4820
7. Borrow P, Lewicki H, Hahn BH, Shaw GM, Oldstone MB (1994) Virus-specific CD8+ cytotoxic T-lymphocyte activity associated with control of viremia in primary human immunodeficiency virus type 1 infection. J Virol 68:6103-6110
8. Chhaya SU (2005) HLA-B27 polymorphism in Mumbai, Western India. Tissue Antigens 66:48-50
9. Chhaya S, Desai S, Saranath D (2010) HLA polymorphisms in Sindhi community in Mumbai, India. Int J Immunogenet 37:373-377
10. Deng Y, Yewdell JW, Eisenlohr LC, Bennink JR (1997) MHC affinity, peptide liberation, T cell repertoire, and immunodominance all contribute to the paucity of MHC class I-restricted peptides recognized by antiviral CTL. J Immunol 158:1507-1515
11. Depla E, Van der Aa A, Livingston BD, Crimi C, Allosery K, De Brabandere V, Krakover J, Murthy S, Huang M, Power S, Babé L, Dahlberg C, McKinney D, Sette A, Southwood S, Philip R, Newman MJ, Meheus L (2008) Rational design of a multiepitope vaccine encoding T-lymphocyte epitopes for treatment of chronic hepatitis B virus infections. J Virol 82:435-450
12. Dönnes P, Kohlbacher O (2006) SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Res 34:W194-W197
13. Feltkamp MC, Vierboom MP, Kast WM, Melief CJ (1994) Efficient MHC class I-peptide binding is required but does not ensure MHC class I-restricted immunogenicity. Mol Immunol 31:1391-1401
14. Gaschen B, Taylor J, Yusim K, Foley B, Gao F, Lang D, Novitsky V, Haynes B, Hahn BH, Bhattacharya T, Korber B (2002) Diversity considerations in HIV-1 vaccine selection. Science 296:2354-2360
15. Hemelaar J, Gouws E, Ghys PD, Osmanov S, WHO-UNAIDS network for HIV isolation and characterisation (2011) Global trends in molecular epidemiology of HIV-1 during 2000-2007. AIDS 25:679-689
16. HIV Molecular Immunology Database. Accessed on September 1, 2011. Available from http://www.hiv. lanl.gov/content/immunology
17. Howles S, Guimarães-Walker A, Yang H, Hancock G, di Gleria K, Tarragona-Fiol T, Hayes P, Gilmour J, Bridgeman A, Hanke T, McMichael A, Dorrell L (2010) Vaccination with a modified vaccinia virus Ankara (MVA)-vectored HIV-1 immunogen induces modest vector-specific T cell responses in human subjects. Vaccine 28:7306-7312
18. Hülsmeyer M, Fiorillo MT, Bettosini F, Sorrentino R, Saenger W, Ziegler A, Uchanska-Ziegler B (2004) Dual, HLA-B27 subtype-dependent conformation of a self-peptide. J Exp Med 199:271-281
19. Immune Epitope Database and Analysis Resource (MHC-I binding predictions). Accessed on 14 June 2012. Available from http://tools. immuneepitope.org/analyze/html/mhc-binding.html
20. International HIV Controllers Study, Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, Walker BD, Ripke S, Brumme CJ, Pulit SL, Carrington M et al (2010) The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 330:1551-1557
21. Jin X, Newman MJ, De-Rosa S, Cooper C, Thomas E, Keefer M, Fuchs J, Blattner W, Livingston BD, McKinney DM, Noonan E, Decamp A, Defawe OD, Wecker M, NIAID HIV Vaccine Trials Network (2009) A novel HIV T helper epitope-based vaccine elicits cytokine-secreting HIV-specific CD4+ T cells in a phase I clinical trial in HIV-uninfected adults. Vaccine 27:7080-7086
22. Kaslow RA, Carrington M, Apple R, Park L, Muñoz A, Saah AJ, Goedert JJ, Winkler C, O'Brien SJ, Rinaldo C, Detels R, Blattner W, Phair J, Erlich H, Mann DL (1996) Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection. Nat Med 2:405-411
23. Kaslow RA, Dorak T, Tang JJ (2005) Influence of host genetic variation on susceptibility to HIV type 1 infection. J Infect Dis 191:S68-S77
24. Kaul R, Dong T, Plummer FA, Kimani J, Rostron T, Kiama P, Njagi E, Irungu E, Farah B, Oyugi J, Chakraborty R, MacDonald KS, Bwayo JJ, McMichael A, Rowland-Jones SL (2001) CD8 (+) lymphocytes respond to different HIV epitopes in seronegative and infected subjects. J Clin Invest 107:1303-1310
25. Kirksey TJ, Pogue-Caley RR, Frelinger JA, Collins EJ (1999) The structural basis for the increased immunogenicity of two HIV-reverse transcriptase peptide variant/class I major histocompati-bility complexes. J Biol Chem 274:37259-37264
26. Kumar N, Mohanty D (2007) MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes. Nucleic Acids Res 35:W549-W555
27. Lafuente EM, Reche PA (2009) Prediction of MHC-peptide binding: a systematic and comprehensive overview. Curr Pharm Des 15:3209-3220
28. Lee JK, Stewart-Jones G, Dong T, Harlos K, Di Gleria K, Dorrell L, Douek DC, van der Merwe PA, Jones EY, McMichael AJ (2004) T cell cross-reactivity and conformational changes during TCR engagement. J Exp Med 200:1455-1466
29. *1101 complexed with immunodominant nonamer and decamer HIV-1 epitopes clearly reveal the presence of a middle, secondary anchor residue. J Immunol 172:6175-6184
30. Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M (2007) Modeling the adaptive immune system: predictions and simulations. Bioinformatics 23:3265-3275
31. Lundegaard C, Lund O, Nielsen M (2008) Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. Bioinformatics 24:1397-1398
32. MacDonald KS, Fowke KR, Kimani J, Dunand VA, Nagelkerke NJ, Ball TB, Oyugi J, Njagi E, Gaur LK, Brunham RC, Wade J, Luscher MA, Krausa P, Rowland-Jones S, Ngugi E, Bwayo JJ, Plummer FA (2000) Influence of HLA supertypes on susceptibility and resistance to human immunodeficiency virus type 1 infection. J Infect Dis 181:1581-1589
33. *5101 complexed with HIV immunodominant epitopes. J Immunol 165:3260-3267
34. McNeil AJ, Yap PL, Gore SM, Brettle RP, McColl M, Wyld R, Davidson S, Weightman R, Richardson AM, Robertson JR (1996) Association of HLA types A1-B8-DR3 and B27 with rapid and slow progression of HIV disease. QJM 89:177-185
35. *5701 is highly associated with restriction of virus replication in a subgroup of HIV-infected long term nonprogressors. Proc Natl Acad Sci U S A 97:2709-2714
36. Moutaftsi M, Peters B, Pasquetto V, Tscharke DC, Sidney J, Bui HH, Grey H, Sette A (2006) A consensus epitope prediction approach identifies the breadth of murine T (CD8+)-cell responses to vaccinia virus. Nat Biotechnol 24:817-819
37. Musey L, Hughes J, Schacker T, Shea T, Corey L, McElrath MJ (1997) Cytotoxic-T-cell responses, viral load, and disease progression in early human immunodeficiency virus type 1 infection. N Engl J Med 337:1267-1274
38. Neumann-Haefelin C (2011) Protective role of HLA-B27 in HIV and hepatitis C virus infection. Dtsch Med Wochenschr 136:320-324
39. *5101 (+) patients protected mice against chimaeric ecotropic HIV-1 challenge. Eur J Immunol 39:1831-1840
40. Ruppert J, Sidney J, Celis E, Kubo RT, Grey HM, Sette A (1993) Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules. Cell 74:929-937
41. Schueler-Furman O, Altuvia Y, Sette A, Margalit H (2000) Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles. Protein Sci 9:1838-1846
42. Selvaraj P, Swaminathan S, Alagarasu K, Raghavan S, Narendran G, Narayanan P (2006) Association of human leukocyte antigen-A11 with resistance and B40 and DR2 with susceptibility to HIV-1 infection in south India. J Acquir Immune Defic Syndr 43:497-499
43. Sette A, Sidney J (1999) Nine major HLA class I supertypes account for the vast preponderance of HLA-A and-B polymorphism. Immunogenetics 50:201-212
44. Sette A, Vitiello A, Reherman B, Fowler P, Nayersina R, Kast WM, Melief CJ, Oseroff C, Yuan L, Ruppert J, Sidney J, del Guercio MF, Southwood S, Kubo RT, Chesnut RW, Grey HM, Chisari FV (1994) The relationship between class I binding affinity and immunogenicity of potential cytotoxic T cell epitopes. J Immunol 153:5586-5592
45. Singh P, Kaur G, Sharma G, Mehra NK (2008) Immunogenetic basis of HIV-1 infection, transmission and disease progression. Vaccine 26:2966-2980
46. *5101 molecules. Hum Immunol 60:177-186
47. van der Burg SH, Visseren MJ, Brandt RM, Kast WM, Melief CJ (1996) Immunogenicity of peptides bound to MHC class I molecules depends on the MHC-peptide complex stability. J Immunol 156:3308-3314
48. Walker BD, Ahmed R, Plotkin S (2011) Moving ahead an HIV vaccine: use both arms to beat HIV. Nat Med 17:1194-1195
49. Wang X, Xie G, Liao J, Yin D, Guan W, Pan M, Li J, Li Y (2011) Design and evaluation of a multi-epitope assembly peptide (MEAP) against herpes simplex virus type 2 infection in BALB/c mice. Virol J 8:232
50. Xiao Y, Lu Y, Chen YH (2001) Epitope-vaccine as a new strategy against HIV-1 mutation. Immunol Lett 77:3-6
51. Zhang Y, Peng Y, Yan H, Xu K, Saito M, Wu H, Chen X, Ranasinghe S, Kuse N, Powell T, Zhao Y, Li W, Zhang X, Feng X, Li N, Leligdowicz A, Xu X, John M, Takiguchi M, McMichael A, Rowland-Jones S, Dong T (2011) Multilayered defense in HLA-B51-associated HIV viral control. J Immunol 187:684-691