HIV Env conserved element DNA vaccine alters immunodominance in macaques

References

• Carlson JM, Brumme CJ, Martin E, Listgarten J, Brockman MA, Le AQ, Chui CK, Cotton LA, Knapp DJ, Riddler SA, et al. Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1. J Virol. 2012;86:13202-16. doi:10.1128/JVI.01998-12. PMID:23055555
   PubMed Web of Science ®Google Scholar
• Carlson JM, Le AQ, Shahid A, Brumme ZL. HIV-1 adaptation to HLA: a window into virus-host immune interactions. Trends Microbiol. 2015;23:212-24. doi:10.1016/j.tim.2014.12.008. PMID:25613992
   PubMed Web of Science ®Google Scholar
• Keane NM, Roberts SG, Almeida CA, Krishnan T, Chopra A, Demaine E, Laird R, Tschochner M, Carlson JM, Mallal S, et al. High-avidity, high-IFNgamma-producing CD8 T-cell responses following immune selection during HIV-1 infection. Immunol Cell Biol. 2012;90:224-34. doi:10.1038/icb.2011.34. PMID:21577229
   PubMed Web of Science ®Google Scholar
• Rolland M, Tovanabutra S, deCamp AC, Frahm N, Gilbert PB, Sanders-Buell E, Heath L, Magaret CA, Bose M, Bradfield A, et al. Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial. Nat Med. 2011;17:366-71. doi:10.1038/nm.2316. PMID:21358627
   PubMed Web of Science ®Google Scholar
• Christie NM, Willer DO, Lobritz MA, Chan JK, Arts EJ, Ostrowski MA, Cochrane A, Luscher MA, MacDonald KS. Viral fitness implications of variation within an immunodominant CD8+ T-cell epitope of HIV-1. Virology. 2009;388:137-46. doi:10.1016/j.virol.2009.03.003. PMID:19368950
   PubMed Web of Science ®Google Scholar
• Brander C, Hartman KE, Trocha AK, Jones NG, Johnson RP, Korber B, Wentworth P, Buchbinder SP, Wolinsky S, Walker BD, et al. 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. 1998;101:2559-66. doi:10.1172/JCI2405. PMID:9616227
   PubMed Web of Science ®Google Scholar
• Herbeck JT, Rolland M, Liu Y, McLaughlin S, McNevin J, Zhao H, Wong K, Stoddard JN, Raugi D, Sorensen S, et al. Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. J Virol. 2011;85:7523-34. doi:10.1128/JVI.02697-10. PMID:21593162
   PubMed Web of Science ®Google Scholar
• Goonetilleke N, Liu MK, Salazar-Gonzalez JF, Ferrari G, Giorgi E, Ganusov VV, Keele BF, Learn GH, Turnbull EL, Salazar MG, et al. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection. J Exp Med. 2009;206:1253-72. doi:10.1084/jem.20090365. PMID:19487423
   PubMed Web of Science ®Google Scholar
• Mullins JI, Nickle DC, Heath L, Rodrigo AG, Learn GH. Immunogen sequence: the fourth tier of AIDS vaccine design. Expert Rev Vaccines. 2004;3:S151-9. doi:10.1586/14760584.3.4.S151. PMID:15285713
   PubMedGoogle Scholar
• Nickle DC, Jensen MA, Gottlieb GS, Shriner D, Learn GH, Rodrigo AG, Mullins JI. Consensus and ancestral state HIV vaccines. Science. 2003;299:1515-8; author reply −8. doi:10.1126/science.299.5612.1515c. PMID:12624248
   PubMed Web of Science ®Google Scholar
• Doria-Rose NA, Learn GH, Rodrigo AG, Nickle DC, Li F, Mahalanabis M, Hensel MT, McLaughlin S, Edmonson PF, Montefiori D, et al. Human immunodeficiency virus type 1 subtype B ancestral envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B envelope. J Virol. 2005;79:11214-24. doi:10.1128/JVI.79.17.11214-11224.2005. PMID:16103173
   PubMed Web of Science ®Google Scholar
• Fischer W, Liao HX, Haynes BF, Letvin NL, Korber B. Coping with viral diversity in HIV vaccine design: a response to Nickle et al. PLoS Comput Biol. 2008;4:e15; author reply e25. doi:10.1371/journal.pcbi.0040015. PMID:18225944
   PubMed Web of Science ®Google Scholar
• Fischer W, Perkins S, Theiler J, Bhattacharya T, Yusim K, Funkhouser R, Kuiken C, Haynes B, Letvin NL, Walker BD, et al. Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nat Med. 2007;13:100-6. doi:10.1038/nm1461. PMID:17187074
   PubMed Web of Science ®Google Scholar
• Barouch DH, O'Brien KL, Simmons NL, King SL, Abbink P, Maxfield LF, Sun YH, La Porte A, Riggs AM, Lynch DM, et al. Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys. Nat Med. 2010;16:319-23. doi:10.1038/nm.2089. PMID:20173752
   PubMed Web of Science ®Google Scholar
• Santra S, Liao HX, Zhang R, Muldoon M, Watson S, Fischer W, Theiler J, Szinger J, Balachandran H, Buzby A, et al. Mosaic vaccines elicit CD8+ T lymphocyte responses that confer enhanced immune coverage of diverse HIV strains in monkeys. Nat Med. 2010;16:324-8. doi:10.1038/nm.2108. PMID:20173754
   PubMed Web of Science ®Google Scholar
• Nickle DC, Jojic N, Heckerman D, Jojic V, Kirovski D, Rolland M, Kosakovsky Pond S, Mullins JI. Comparison of immunogen designs that optimize peptide coverage: reply to Fischer et al. PLoS Comput Biol. 2008;4:e25. doi:10.1371/journal.pcbi.0040025. PMID:18463692
   PubMed Web of Science ®Google Scholar
• Nickle DC, Rolland M, Jensen MA, Pond SL, Deng W, Seligman M, Heckerman D, Mullins JI, Jojic N. Coping with viral diversity in HIV vaccine design. PLoS Comput Biol. 2007;3:e75. doi:10.1371/journal.pcbi.0030075. PMID:17465674
   PubMed Web of Science ®Google Scholar
• Hu X, Valentin A, Dayton F, Kulkarni V, Alicea A, Rosati M, Chowdhury B, Gautam R, Broderick KE, Sardesai NY, et al. DNA Prime-boost Vaccine Regimen to Increase Breadth, Magnitude, and Cytotoxicity of the Cellular Immune Responses to Subdominant Gag Epitopes of SIV and HIV. J Immunol. 2016;197:3999-4013. doi:10.4049/jimmunol.1600697. PMID:27733554
   PubMed Web of Science ®Google Scholar
• Kulkarni V, Rosati M, Valentin A, Ganneru B, Singh AK, Yan J, Rolland M, Alicea C, Beach RK, Zhang GM, et al. HIV-1 p24gag derived conserved element DNA vaccine increases the breadth of immune response in mice. PLos One. 2013;8:e60245. doi:10.1371/journal.pone.0060245. PMID:23555935
   PubMed Web of Science ®Google Scholar
• Kulkarni V, Valentin A, Rosati M, Alicea C, Singh AK, Jalah R, Broderick KE, Sardesai NY, Le Gall S, Mothe B, et al. Altered response hierarchy and increased T-cell breadth upon HIV-1 conserved element DNA vaccination in macaques. PLoS One. 2014;9:e86254. doi:10.1371/journal.pone.0086254. PMID:24465991
   PubMed Web of Science ®Google Scholar
• Kulkarni V, Valentin A, Rosati M, Rolland M, Mullins JI, Pavlakis GN, Felber BK. HIV-1 Conserved elements p24CE DNA vaccine induces humoral immune responses with broad epitope recognition in macaques. PLoS One. 2014;9:e111085. doi:10.1371/journal.pone.0111085. PMID:25338098
   PubMed Web of Science ®Google Scholar
• Mothe B, Hu X, Llano A, Rosati M, Olvera A, Kulkarni V, Valentin A, Alicea C, Pilkington GR, Sardesai NY, et al. A human immune data-informed vaccine concept elicits strong and broad T-cell specificities associated with HIV-1 control in mice and macaques. J Transl Med. 2015;13:60. doi:10.1186/s12967-015-0392-5. PMID:25879820
   PubMed Web of Science ®Google Scholar
• Letourneau S, Im EJ, Mashishi T, Brereton C, Bridgeman A, Yang H, Dorrell L, Dong T, Korber B, McMichael AJ, et al. Design and pre-clinical evaluation of a universal HIV-1 vaccine. PLoS One. 2007;2:e984. doi:10.1371/journal.pone.0000984. PMID:17912361
   PubMed Web of Science ®Google Scholar
• Ondondo B, Murakoshi H, Clutton G, Abdul-Jawad S, Wee EG, Gatanaga H, Oka S, McMichael AJ, Takiguchi M, Korber B, et al. Novel conserved-region T-cell mosaic vaccine with high global HIV-1 coverage is recognized by protective responses in untreated infection. Mol Ther. 2016;24:832-42. doi:10.1038/mt.2016.3. PMID:26743582
   PubMed Web of Science ®Google Scholar
• Kran AM, Sorensen B, Nyhus J, Sommerfelt MA, Baksaas I, Bruun JN, Kvale D. HLA- and dose-dependent immunogenicity of a peptide-based HIV-1 immunotherapy candidate (Vacc-4x). AIDS. 2004;18:1875-83. doi:10.1097/00002030-200409240-00003. PMID:15353973
   PubMed Web of Science ®Google Scholar
• Mothe B, Llano A, Ibarrondo J, Zamarreno J, Schiaulini M, Miranda C, Ruiz-Riol M, Berger CT, Herrero MJ, Palou E, et al. CTL responses of high functional avidity and broad variant cross-reactivity are associated with HIV control. PLoS One. 2012;7:e29717. doi:10.1371/journal.pone.0029717. PMID:22238642
   PubMed Web of Science ®Google Scholar
• Rolland M, Jensen MA, Nickle DC, Yan J, Learn GH, Heath L, Weiner D, Mullins JI. Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteins. J Virol. 2007;81:8507-14. doi:10.1128/JVI.02683-06. PMID:17537854
   PubMed Web of Science ®Google Scholar
• Rolland M, Manocheewa S, Swain JV, Lanxon-Cookson EC, Kim M, Westfall DH, Larsen BB, Gilbert PB, Mullins JI. HIV-1 conserved-element vaccines: relationship between sequence conservation and replicative capacity. J Virol. 2013;87:5461-7. doi:10.1128/JVI.03033-12. PMID:23468488
   PubMed Web of Science ®Google Scholar
• Rolland M, Nickle DC, Mullins JI. HIV-1 group M conserved elements vaccine. PLoS Pathog. 2007;3:e157. doi:10.1371/journal.ppat.0030157. PMID:18052528
   PubMed Web of Science ®Google Scholar
• Khan AS, Broderick KE, Sardesai NY. Clinical development of intramuscular electroporation: providing a “boost” for DNA vaccines. Methods Mol Biol. 2014;1121:279-89; PMID:24510832
   PubMedGoogle Scholar
• Felber BK, Valentin A, Rosati M, Bergamaschi C, Pavlakis GN. HIV DNA Vaccine: Stepwise improvements make a difference. Vaccines. 2014;2:354-79. doi:10.3390/vaccines2020354. PMID:26344623
   PubMedGoogle Scholar
• Rose PP, Korber BT. Detecting hypermutations in viral sequences with an emphasis on G –>A hypermutation. Bioinformatics. 2000;16:400-1. doi:10.1093/bioinformatics/16.4.400. PMID:10869039
   PubMed Web of Science ®Google Scholar
• Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004;5:113. doi:10.1186/1471-2105-5-113. PMID:15318951
   PubMed Web of Science ®Google Scholar
• Le Gall S, Stamegna P, Walker BD. Portable flanking sequences modulate CTL epitope processing. J Clin Invest. 2007;117:3563-75. doi:10.1172/JCI32047. PMID:17975674
   PubMed Web of Science ®Google Scholar
• Zhang SC, Martin E, Shimada M, Godfrey SB, Fricke J, Locastro S, Lai NY, Liebesny P, Carlson JM, Brumme CJ, et al. Aminopeptidase substrate preference affects HIV epitope presentation and predicts immune escape patterns in HIV-infected individuals. J Immunol. 2012;188:5924-34. doi:10.4049/jimmunol.1200219. PMID:22586036
   PubMed Web of Science ®Google Scholar
• Rosati M, von Gegerfelt A, Roth P, Alicea C, Valentin A, Robert-Guroff M, Venzon D, Montefiori DC, Markham P, Felber BK, et al. DNA vaccines expressing different forms of simian immunodeficiency virus antigens decrease viremia upon SIVmac251 challenge. J Virol. 2005;79:8480-92. doi:10.1128/JVI.79.13.8480-8492.2005. PMID:15956591
   PubMed Web of Science ®Google Scholar
• Kopycinski J, Cheeseman H, Ashraf A, Gill D, Hayes P, Hannaman D, Gilmour J, Cox JH, Vasan S. A DNA-based candidate HIV vaccine delivered via in vivo electroporation induces CD4 responses toward the alpha4beta7-binding V2 loop of HIV gp120 in healthy volunteers. Clin Vaccine Immunol. 2012;19:1557-9; PMID:22837097
   PubMed Web of Science ®Google Scholar
• Harari A, Bart PA, Stohr W, Tapia G, Garcia M, Medjitna-Rais E, Burnet S, Cellerai C, Erlwein O, Barber T, et al. An HIV-1 clade C DNA prime, NYVAC boost vaccine regimen induces reliable, polyfunctional, and long-lasting T cell responses. J Exp Med. 2008;205:63-77; PMID:18195071
   PubMed Web of Science ®Google Scholar
• Rerks-Ngarm S, Pitisuttithum P, Nitayaphan S, Kaewkungwal J, Chiu J, Paris R, Premsri N, Namwat C, de Souza M, Adams E, et al. Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand. N Engl J Med. 2009;361:2209-20; PMID:19843557
   PubMed Web of Science ®Google Scholar
• de Souza MS, Ratto-Kim S, Chuenarom W, Schuetz A, Chantakulkij S, Nuntapinit B, Valencia-Micolta A, Thelian D, Nitayaphan S, Pitisuttithum P, et al. The Thai phase III trial (RV144) vaccine regimen induces T cell responses that preferentially target epitopes within the V2 region of HIV-1 envelope. J Immunol. 2012;188:5166-76; PMID:22529301
   PubMed Web of Science ®Google Scholar
• Orentas RJ, Hildreth JE, Obah E, Polydefkis M, Smith GE, Clements ML, Siliciano RF. Induction of CD4+ human cytolytic T cells specific for HIV-infected cells by a gp160 subunit vaccine. Science. 1990;248:1234-7; PMID:2190315
   PubMed Web of Science ®Google Scholar
• Li J, Valentin A, Kulkarni V, Rosati M, Beach RK, Alicea C, Hannaman D, Reed SG, Felber BK, Pavlakis GN. HIV/SIV DNA vaccine combined with protein in a Co-immunization protocol elicits highest humoral responses to envelope in mice and macaques. Vaccine. 2013;31:3747-55
   PubMed Web of Science ®Google Scholar
• Patel V, Jalah R, Kulkarni V, Valentin A, Rosati M, Alicea C, von Gegerfelt A, Huang W, Guan Y, Keele BF, et al. DNA and virus particle vaccination protects against acquisition and confers control of viremia upon heterologous SIV challenge. Proc Natl Acad Sci U S A. 2013;110:2975-80
   PubMed Web of Science ®Google Scholar