In silico design of a DNA-based HIV-1 multi-epitope vaccine for Chinese populations

References

• Barre-Sinoussi F, Chermann JC, Rey F, Nugeyre MT, Chamaret S, Gruest J, Dauguet C, Axler-Blin C, Vezinet-Brun F, Rouzioux C, et al. Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science (New York, NY) 1983; 220:868–71; http://dx.doi.org/10.1126/science.6189183
   Web of Science ®Google Scholar
• Wei X, Decker JM, Wang S, Hui H, Kappes JC, Wu X, Salazar-Gonzalez JF, Salazar MG, Kilby JM, Saag MS, et al. Antibody neutralization and escape by HIV-1. Nature 2003; 422:307-12; PMID:12646921; http://dx.doi.org/10.1038/nature01470
   PubMed Web of Science ®Google Scholar
• Klein JS, Bjorkman PJ. Few and far between: how HIV may be evading antibody avidity. PLoS Pathogens 2010; 6:e1000908; PMID:20523901; http://dx.doi.org/10.1371/journal.ppat.1000908
   PubMed Web of Science ®Google Scholar
• Goulder PJ, Walker BD. HIV and HLA class I: an evolving relationship. Immunity 2012; 37:426-40; PMID:22999948; http://dx.doi.org/10.1016/j.immuni.2012.09.005
   PubMed Web of Science ®Google Scholar
• Stern LJ, Calvo-Calle JM. HLA-DR: molecular insights and vaccine design. Curr Pharm Des 2009; 15:3249-61; PMID:19860674; http://dx.doi.org/10.2174/138161209789105171
   PubMed Web of Science ®Google Scholar
• Moore CB, John M, James IR, Christiansen FT, Witt CS, Mallal SA. Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science (New York, NY) 2002; 296:1439-43; http://dx.doi.org/10.1126/science.1069660
   Web of Science ®Google Scholar
• Johnston MI, Fauci AS. An HIV vaccine–evolving concepts. N Engl J Med 2007; 356:2073-81; PMID:17507706; http://dx.doi.org/10.1056/NEJMra066267
   PubMed Web of Science ®Google Scholar
• Spearman P. Current progress in the development of HIV vaccines. Curr Pharm Des 2006; 12:1147-67; PMID:16515492; http://dx.doi.org/10.2174/138161206776055859
   PubMed Web of Science ®Google Scholar
• Li C, Shen Z, Li X, Bai J, Zeng L, Tian M, Song YJ, Ye M, Du S, Ren D, et al. Protection against SHIV-KB9 infection by combining rDNA and rFPV vaccines based on HIV multiepitope and p24 protein in Chinese rhesus macaques. Clin Dev Immunol 2012; 2012:958404; PMID:22474488
   PubMedGoogle Scholar
• Gilbert P, Wang M, Wrin T, Petropoulos C, Gurwith M, Sinangil F, D'Souza P, Rodriguez-Chavez IR, DeCamp A, Giganti M, et al. Magnitude and breadth of a nonprotective neutralizing antibody response in an efficacy trial of a candidate HIV-1 gp120 vaccine. J Infect Dis 2010; 202:595-605; PMID:20608874; http://dx.doi.org/10.1086/654816
   PubMed Web of Science ®Google Scholar
• McCoy LE, Weiss RA. Neutralizing antibodies to HIV-1 induced by immunization. J Exp Med 2013; 210:209-23; PMID:23401570; http://dx.doi.org/10.1084/jem.20121827
   PubMed Web of Science ®Google Scholar
• Karnasuta C, Paris RM, Cox JH, Nitayaphan S, Pitisuttithum P, Thongcharoen P, Brown AE, Gurunathan S, Tartaglia J, Heyward WL, et al. Antibody-dependent cell-mediated cytotoxic responses in participants enrolled in a phase I/II ALVAC-HIV/AIDSVAX B/E prime-boost HIV-1 vaccine trial in Thailand. Vaccine 2005; 23:2522-9; PMID:15752839; http://dx.doi.org/10.1016/j.vaccine.2004.10.028
   PubMed Web of Science ®Google Scholar
• Shacklett BL, Ferre AL. Mucosal immunity in HIV controllers: the right place at the right time. Curr Opin HIV AIDS 2011; 6:202-7; PMID:21399497; http://dx.doi.org/10.1097/COH.0b013e3283453e2b
   PubMedGoogle Scholar
• Mudd PA, Watkins DI. Understanding animal models of elite control: windows on effective immune responses against immunodeficiency viruses. Curr Opin HIV AIDS 2011; 6:197-201; PMID:21502922; http://dx.doi.org/10.1097/COH.0b013e3283453e16
   PubMedGoogle Scholar
• Munier CM, Kelleher AD, Kent SJ, De Rose R. The role of T cell immunity in HIV-1 infection. Curr Opin Virol 2013; 3:438-46; PMID:23747036; http://dx.doi.org/10.1016/j.coviro.2013.05.009
   PubMed Web of Science ®Google Scholar
• Perrin H, Canderan G, Sekaly RP, Trautmann L. New approaches to design HIV-1 T-cell vaccines. Curr Opin HIV AIDS 2010; 5:368-76; PMID:20978376; http://dx.doi.org/10.1097/COH.0b013e32833d2cc0
   PubMedGoogle Scholar
• Kunwar P, Hawkins N, Dinges WL, Liu Y, Gabriel EE, Swan DA, Stevens CE, Maenza J, Collier AC, Mullins JI, et al. Superior control of HIV-1 replication by CD8+ T cells targeting conserved epitopes: implications for HIV vaccine design. PloS One 2013; 8:e64405; PMID:23741326; http://dx.doi.org/10.1371/journal.pone.0064405
   PubMed Web of Science ®Google Scholar
• Levitz L, Koita OA, Sangare K, Ardito MT, Boyle CM, Rozehnal J, Tounkara K, Dao SM, Kone Y, Koty Z, et al. Conservation of HIV-1 T cell epitopes across time and clades: validation of immunogenic HLA-A2 epitopes selected for the GAIA HIV vaccine. Vaccine 2012; 30:7547-60; PMID:23102976; http://dx.doi.org/10.1016/j.vaccine.2012.10.042
   PubMed Web of Science ®Google Scholar
• De Groot AS, Rivera DS, McMurry JA, Buus S, Martin W. Identification of immunogenic HLA-B7 “Achilles' heel” epitopes within highly conserved regions of HIV. Vaccine 2008; 26:3059-71; PMID:18206276; http://dx.doi.org/10.1016/j.vaccine.2007.12.004
   PubMedGoogle Scholar
• Goulder PJ, Watkins DI. HIV and SIV CTL escape: implications for vaccine design. Nat Rev Immunol 2004; 4:630-40; PMID:15286729; http://dx.doi.org/10.1038/nri1417
   PubMed Web of Science ®Google Scholar
• Rodriguez F, Harkins S, Slifka MK, Whitton JL. Immunodominance in virus-induced CD8(+) T-cell responses is dramatically modified by DNA immunization and is regulated by gamma interferon. J Virol 2002; 76:4251-9; PMID:11932390; http://dx.doi.org/10.1128/JVI.76.9.4251-4259.2002
   PubMedGoogle Scholar
• Im EJ, Hong JP, Roshorm Y, Bridgeman A, Letourneau S, Liljestrom P, Potash MJ, Volsky DJ, McMichael AJ, Hanke T. Protective efficacy of serially up-ranked subdominant CD8+ T cell epitopes against virus challenges. PLoS Pathogens 2011; 7:e1002041; PMID:21625575; http://dx.doi.org/10.1371/journal.ppat.1002041
   PubMed Web of Science ®Google Scholar
• Manuel ER, Yeh WW, Seaman MS, Furr K, Lifton MA, Hulot SL, Autissier P, Letvin NL. Dominant CD8+ T-lymphocyte responses suppress expansion of vaccine-elicited subdominant T lymphocytes in rhesus monkeys challenged with pathogenic simian-human immunodeficiency virus. J Virol 2009; 83:10028-35; PMID:19641002; http://dx.doi.org/10.1128/JVI.01015-09
   PubMedGoogle Scholar
• Gorse GJ, Baden LR, Wecker M, Newman MJ, Ferrari G, Weinhold KJ, Livingston BD, Villafana TL, Li H, Noonan E, et al. Safety and immunogenicity of cytotoxic T-lymphocyte poly-epitope, DNA plasmid (EP HIV-1090) vaccine in healthy, human immunodeficiency virus type 1 (HIV-1)-uninfected adults. Vaccine 2008; 26:215-23; PMID:18055072; http://dx.doi.org/10.1016/j.vaccine.2007.10.061
   PubMedGoogle Scholar
• Jin X, Newman MJ, De-Rosa S, Cooper C, Thomas E, Keefer M, Fuchs J, Blattner W, Livingston BD, McKinney DM, et al. 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 2009; 27:7080-6; PMID:19786145; http://dx.doi.org/10.1016/j.vaccine.2009.09.060
   PubMed Web of Science ®Google Scholar
• Spearman P, Kalams S, Elizaga M, Metch B, Chiu YL, Allen M, Weinhold KJ, Ferrari G, Parker SD, McElrath MJ, et al. Safety and immunogenicity of a CTL multiepitope peptide vaccine for HIV with or without GM-CSF in a phase I trial. Vaccine 2009; 27:243-9; PMID:18996425; http://dx.doi.org/10.1016/j.vaccine.2008.10.051
   PubMed Web of Science ®Google Scholar
• Paul S, Piontkivska H. Discovery of novel targets for multi-epitope vaccines: screening of HIV-1 genomes using association rule mining. Retrovirology 2009; 6:62; PMID:19580659; http://dx.doi.org/10.1186/1742-4690-6-62
   PubMedGoogle Scholar
• Wilson CC, Newman MJ, Livingston BD, MaWhinney S, Forster JE, Scott J, Schooley RT, Benson CA. Clinical phase 1 testing of the safety and immunogenicity of an epitope-based DNA vaccine in human immunodeficiency virus type 1-infected subjects receiving highly active antiretroviral therapy. Clin Vaccine Immunol 2008; 15:986-94; PMID:18400976; http://dx.doi.org/10.1128/CVI.00492-07
   PubMedGoogle Scholar
• Paul S, Piontkivska H. Frequent associations between CTL and T-Helper epitopes in HIV-1 genomes and implications for multi-epitope vaccine designs. BMC Microbiol 2010; 10:212; PMID:20696039; http://dx.doi.org/10.1186/1471-2180-10-212
   PubMedGoogle Scholar
• Hemelaar J, Gouws E, Ghys PD, Osmanov S. Global trends in molecular epidemiology of HIV-1 during 2000-2007. AIDS (London, England) 2011; 25:679-89; PMID:21297424; http://dx.doi.org/10.1097/QAD.0b013e328342ff93
   PubMed Web of Science ®Google Scholar
• Trachtenberg E, Vinson M, Hayes E, Hsu YM, Houtchens K, Erlich H, Klitz W, Hsia Y, Hollenbach J. HLA class I (A, B, C) and class II (DRB1, DQA1, DQB1, DPB1) alleles and haplotypes in the Han from southern China. Tissue Antigens 2007; 70:455-63; PMID:17900288; http://dx.doi.org/10.1111/j.1399-0039.2007.00932.x
   PubMedGoogle Scholar
• Li XF, Zhang X, Chen Y, Zhang KL, Liu XJ, Li JP. An analysis of HLA-A, -B, and -DRB1 allele and haplotype frequencies of 21,918 residents living in Liaoning, China. PloS One 2014; 9:e93082; PMID:24691290; http://dx.doi.org/10.1371/journal.pone.0093082
   PubMedGoogle Scholar
• Girard MP, Osmanov S, Assossou OM, Kieny MP. Human immunodeficiency virus (HIV) immunopathogenesis and vaccine development: a review. Vaccine 2011; 29:6191-218; PMID:21718747; http://dx.doi.org/10.1016/j.vaccine.2011.06.085
   PubMed Web of Science ®Google Scholar
• Smahel M, Polakova I, Duskova M, Ludvikova V, Kastankova I. The effect of helper epitopes and cellular localization of an antigen on the outcome of gene gun DNA immunization. Gene Ther 2014; 21:225-32; PMID:24385146; http://dx.doi.org/10.1038/gt.2013.81
   PubMed Web of Science ®Google Scholar
• Kumar A, Arora R, Kaur P, Chauhan VS, Sharma P. “Universal" T helper cell determinants enhance immunogenicity of a Plasmodium falciparum merozoite surface antigen peptide. J Immunol 1992; 148:1499-505; PMID:1371529
   PubMed Web of Science ®Google Scholar
• Soghoian DZ, Jessen H, Flanders M, Sierra-Davidson K, Cutler S, Pertel T, Ranasinghe S, Lindqvist M, Davis I, Lane K, et al. HIV-specific cytolytic CD4 T cell responses during acute HIV infection predict disease outcome. Sci Transl Med 2012; 4:123ra25; PMID:22378925; http://dx.doi.org/10.1126/scitrans-lmed.3003165
   PubMed Web of Science ®Google Scholar
• Soghoian DZ, Streeck H. Cytolytic CD4(+) T cells in viral immunity. Expert Rev Vaccines 2010; 9:1453-63; PMID:21105780; http://dx.doi.org/10.1586/erv.10.132
   PubMed Web of Science ®Google Scholar
• Chang CX, Tan AT, Or MY, Toh KY, Lim PY, Chia AS, Froesig TM, Nadua KD, Oh HL, Leong HN, et al. Conditional ligands for Asian HLA variants facilitate the definition of CD8+ T-cell responses in acute and chronic viral diseases. Eur J Immunol 2013; 43:1109-20; PMID:23280567; http://dx.doi.org/10.1002/eji.201243088
   PubMedGoogle Scholar
• Reddy Chichili VP, Kumar V, Sivaraman J. Linkers in the structural biology of protein-protein interactions. Protein Sci 2013; 22:153-67; PMID:23225024; http://dx.doi.org/10.1002/pro.2206
   PubMed Web of Science ®Google Scholar
• Deane JE, Ryan DP, Sunde M, Maher MJ, Guss JM, Visvader JE, Matthews JM. Tandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex. EMBO J 2004; 23:3589-98; PMID:15343268; http://dx.doi.org/10.1038/sj.emboj.7600376
   PubMedGoogle Scholar
• Wang QM, Sun SH, Hu ZL, Zhou FJ, Yin M, Xiao CJ, Zhang JC. Epitope DNA vaccines against tuberculosis: spacers and ubiquitin modulates cellular immune responses elicited by epitope DNA vaccine. Scand J Immunol 2004; 60:219-25; PMID:15320877; http://dx.doi.org/10.1111/j.0300-9475.2004.01442.x
   PubMed Web of Science ®Google Scholar
• Velders MP, Weijzen S, Eiben GL, Elmishad AG, Kloetzel PM, Higgins T, Ciccarelli RB, Evans M, Man S, Smith L, et al. Defined flanking spacers and enhanced proteolysis is essential for eradication of established tumors by an epitope string DNA vaccine. J Immunol 2001; 166:5366-73; PMID:11313372; http://dx.doi.org/10.4049/jimmunol.166.9.5366
   PubMed Web of Science ®Google Scholar