title: Optimization and immune recognition of multiple novel conserved HLA-A2, human immunodeficiency virus type 1-specific CTL epitopes.
abstract: MHC-I-restricted cytotoxic responses are considered a critical component of protective immunity against viruses, including human immunodeficiency virus type 1 (HIV-1). CTLs directed against accessory and early regulatory HIV-1 proteins might be particularly effective; however, CTL epitopes in these proteins are rarely found. Novel artificial neural networks (ANNs) were used to quantitatively predict HLA-A2-binding CTL epitope peptides from publicly available full-length HIV-1 protein sequences. Epitopes were selected based on their novelty, predicted HLA-A2-binding affinity and conservation among HIV-1 strains. HLA-A2 binding was validated experimentally and binders were tested for their ability to induce CTL and IFN-gamma responses. About 69 % were immunogenic in HLA-A2 transgenic mice and 61 % were recognized by CD8(+) T-cells from 17 HLA-A2 HIV-1-positive patients. Thus, 31 novel conserved CTL epitopes were identified in eight HIV-1 proteins, including the first HLA-A2 minimal epitopes ever reported in the accessory and regulatory proteins Vif, Vpu and Rev. Interestingly, intermediate-binding peptides of low or no immunogenicity (i.e. subdominant epitopes) were found to be antigenic and more conserved. Such epitope peptides were anchor-optimized to improve immunogenicity and further increase the number of potential vaccine epitopes. About 67 % of anchor-optimized vaccine epitopes induced immune responses against the corresponding non-immunogenic naturally occurring epitopes. This study demonstrates the potency of ANNs for identifying putative virus CTL epitopes, and the new HIV-1 CTL epitopes identified should have significant implications for HIV-1 vaccine development. As a novel vaccine approach, it is proposed to increase the coverage of HIV variants by including multiple anchor-optimized variants of the more conserved subdominant epitopes.
authors.affiliation: Department of Virology, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen S, Denmark.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Corbet
authors.affiliation: Department of Virology, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen S, Denmark.
authors.forename: Henrik Vedel
authors.initials: HV
authors.lastname: Nielsen
authors.affiliation: Department of Virology, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen S, Denmark.
authors.forename: Lasse
authors.initials: L
authors.lastname: Vinner
authors.affiliation: Institute for Medical Microbiology and Immunology, University of Copenhagen, Denmark.
authors.forename: Sanne
authors.initials: S
authors.lastname: Lauemoller
authors.affiliation: Department of Virology, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen S, Denmark.
authors.forename: Dominic
authors.initials: D
authors.lastname: Therrien
authors.affiliation: Department of Virology, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen S, Denmark.
authors.forename: Sheila
authors.initials: S
authors.lastname: Tang
authors.affiliation: Department of Infectious Diseases, University Hospital of Copenhagen, Denmark.
authors.forename: Gitte
authors.initials: G
authors.lastname: Kronborg
authors.affiliation: Department of Infectious Diseases, University Hospital of Hvidovre, Denmark.
authors.forename: Lars
authors.initials: L
authors.lastname: Mathiesen
authors.affiliation: Bavarian Nordic Research Institute, Martinsried, Germany.
authors.forename: Paul
authors.initials: P
authors.lastname: Chaplin
authors.affiliation: Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.affiliation: Institute for Medical Microbiology and Immunology, University of Copenhagen, Denmark.
authors.forename: Søren
authors.initials: S
authors.lastname: Buus
authors.affiliation: Department of Virology, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen S, Denmark.
authors.forename: Anders
authors.initials: A
authors.lastname: Fomsgaard
mesh_terms: D000328:Adult; D000818:Animals; D018414:CD8-Positive T-Lymphocytes / Q000276:immunology; D018984:Epitopes, T-Lymphocyte; D005260:Female; D015694:Gene Products, rev / Q000276:immunology; D016346:Gene Products, vif / Q000276:immunology; D015658:HIV Infections / Q000097:blood / Q000276:immunology*; D015497:HIV-1 / Q000737:chemistry / Q000276:immunology*; D015789:HLA-A2 Antigen / Q000235:genetics / Q000276:immunology*; D054298:Human Immunodeficiency Virus Proteins; D006801:Humans; D008297:Male; D051379:Mice; D008822:Mice, Transgenic; D008875:Middle Aged; D009842:Oligopeptides / Q000032:analysis; D013045:Species Specificity; D013602:T-Lymphocytes, Cytotoxic / Q000276:immunology*; D054334:Viral Regulatory and Accessory Proteins / Q000276:immunology; D054321:rev Gene Products, Human Immunodeficiency Virus; D054320:vif Gene Products, Human Immunodeficiency Virus; D000086082:Viroporin Proteins
chemical_list: D018984:Epitopes, T-Lymphocyte; D015694:Gene Products, rev; D016346:Gene Products, vif; D015789:HLA-A2 Antigen; D054298:Human Immunodeficiency Virus Proteins; D009842:Oligopeptides; D054334:Viral Regulatory and Accessory Proteins; D054321:rev Gene Products, Human Immunodeficiency Virus; D054320:vif Gene Products, Human Immunodeficiency Virus; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins