title: Engineering immunogenic consensus T helper epitopes for a cross-clade HIV vaccine.
abstract: Developing a vaccine that will stimulate broad HIV-specific T cell responses is difficult because of the variability in HIV T cell epitope sequences, which is in turn due to the high mutation rate and consequent strain diversity of HIV-1. We used a new Class II version of the EpiMatrix T cell epitope-mapping tool and Conservatrix to select highly conserved and promiscuous Class II HLA-restricted T cell epitopes from a database of 18,313 HIV-1 env sequences. Criteria for selection were: (1) number of HIV-1 strains represented as measured by Conservatrix; (2) EpiMatrix score; and (3) promiscuity (number of unique MHC motifs contained in the peptide). Using another vaccine design tool called the EpiAssembler, a new set of overlapping, conserved and immunogenic HIV-1 peptides were engineered creating extended "immunogenic consensus" sequences. Each overlapping 9-mer of the 20-23 amino acid long immunogenic consensus peptides was conserved in a large number (range 893-2254) of individual HIV-1 strains, although the novel peptides were not representative of any single strain of HIV. We synthesized nine representative peptides. T helper cell responses to the peptides were evaluated by ELISpot (gamma-interferon) assay, using peripheral blood monocytes (PBMC) obtained from 34 healthy long term non-progressor (LT) or moderate-progressor (MP) donors (median years infected = 8.88, median CD4 T cells = 595, median VL = 1044). Nine peptides were tested, of which eight were confirmed in ELISpot assays using PBMC from the LT/MP subjects. These epitopes were ranked by Conservation and EpiMatrix score 1, 2, 3, 5, 7, 11, and 14 out of the set of 9 original peptides. Five of these peptides were selected for inclusion in an epitope-driven cross-clade HIV-1 vaccine (the GAIA vaccine). These data confirm the utility of bioinformatics tools to select and construct novel "immunogenic consensus sequence" T cell epitopes for a globally relevant vaccine against HIV.
authors.affiliation: TB/HIV Research Lab, Brown University, Providence RI 02912, USA. AnnieD@Brown.edu
authors.forename: Anne S
authors.initials: AS
authors.lastname: De Groot
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Bishop
authors.forename: Basim
authors.initials: B
authors.lastname: Khan
authors.forename: Michelle
authors.initials: M
authors.lastname: Lally
authors.forename: Luisa
authors.initials: L
authors.lastname: Marcon
authors.forename: Judith
authors.initials: J
authors.lastname: Franco
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Mayer
authors.forename: Charles C J
authors.initials: CC
authors.lastname: Carpenter
authors.forename: William
authors.initials: W
authors.lastname: Martin
mesh_terms: D016915:AIDS Vaccines / Q000235:genetics* / Q000276:immunology; D000465:Algorithms; D000595:Amino Acid Sequence; D015331:Cohort Studies; D016384:Consensus Sequence; D018604:Epitope Mapping / Q000379:methods*; D018984:Epitopes, T-Lymphocyte / Q000235:genetics* / Q000276:immunology; D015497:HIV-1 / Q000235:genetics* / Q000276:immunology; D006801:Humans; D008969:Molecular Sequence Data; D010455:Peptides / Q000138:chemical synthesis; D010865:Pilot Projects; D020539:Sequence Analysis, Protein / Q000379:methods; D006377:T-Lymphocytes, Helper-Inducer / Q000276:immunology* / Q000378:metabolism*
chemical_list: D016915:AIDS Vaccines; D018984:Epitopes, T-Lymphocyte; D010455:Peptides