title: An unanticipated lack of consensus cytotoxic T lymphocyte epitopes in HIV-1 databases: the contribution of prediction programs.
abstract: BACKGROUND
  Most consensus HIV-1-specific cytotoxic T lymphocytes epitopes presented via intensively studied HLA molecules are thought to be known
  
  
  OBJECTIVE
  To identify possible novel HIV-1 epitopes for HLA-B27 and HLA-B57; two HLA types which are abundantly studied because of their correlation with slow HIV disease progression.
  
  
  METHODS
  HIV-1 consensus subtype B sequences were analysed using peptide prediction programs based on major histocompatibility complex binding, proteasomal cleavage and TAP (transporter associated with antigen processing) transport. Recognition of the novel identified epitopes by cytotoxic T lymphocytes was tested using interferon-gamma ELISpot assay.
  
  
  RESULTS
  In total, 22 novel epitopes predicted to be presented by either HLA-B27 or HLA-B57 were selected. Of these, 86% elicited significant immune responses in HIV-1-infected individuals.
  
  
  CONCLUSIONS
  These data show that numerous HIV-1 epitopes remain to be identified, and that prediction programs are powerful tools for this purpose.
authors: Department of Immunology, University Medical Center, the Netherlands.
authors: Ingrid M M
authors: IM
authors: Schellens
authors: Can
authors: C
authors: Keşmir
authors: Frank
authors: F
authors: Miedema
authors: Debbie
authors: D
authors: van Baarle
authors: José A M
authors: JA
authors: Borghans
mesh_terms: D018528:ATP-Binding Cassette Transporters; D030541:Databases, Genetic; D018604:Epitope Mapping; D018984:Epitopes, T-Lymphocyte / Q000032:analysis* / Q000235:genetics; D015658:HIV Infections / Q000276:immunology*; D015497:HIV-1 / Q000235:genetics / Q000276:immunology*; D015235:HLA-B Antigens / Q000276:immunology; D015796:HLA-B27 Antigen / Q000276:immunology; D006801:Humans; D010455:Peptides; D013045:Species Specificity; D013602:T-Lymphocytes, Cytotoxic / Q000276:immunology*
chemical_list: D018528:ATP-Binding Cassette Transporters; D018984:Epitopes, T-Lymphocyte; D015235:HLA-B Antigens; D015796:HLA-B27 Antigen; C103707:HLA-B57 antigen; D010455:Peptides; C477327:transporter associated with antigen processing (TAP)