title: Impact of intrapeptide epitope location on CD8 T cell recognition: implications for design of overlapping peptide panels.
abstract: BACKGROUND
  Antigen-specific CD8 T cells following infection or immunization are typically assessed by measuring interferon-gamma production after stimulation with overlapping peptides spanning the region of interest. The effect of epitope location within such peptides is not known but may influence recognition.
  
  
  OBJECTIVE
  To examine if peptides containing the appropriate C-terminal anchor amino acid residue would provide more sensitive detection of T cell responses. The impact was examined of epitope location within overlapping peptides on recognition of epitope-specific CD8 T cell responses.
  
  
  METHODS
  C-terminal amino acid residues were analyzed in well-defined optimal epitopes for HIV, Epstein-Barr virus, cytomegalovirus and influenza and in peptide-binding motifs. Recognition of known epitopes within longer synthesized peptides by peripheral blood mononuclear cells or CD8 T cell lines was tested using interferon-gamma Elispot at various peptide concentrations.
  
  
  RESULTS
  Only 9 of 20 amino acids served as the C-terminal anchor position in 96% of described optimal epitopes and in 95% of peptide-binding motifs. A CD8 T cell response to an epitope within a longer peptide is best detected when the epitope is situated at the C-terminal end of the longer peptide, both when using peptides designed to include the optimal epitope at every possible position and when comparing responses towards optimal epitopes and corresponding overlapping peptides in a larger group of subjects.
  
  
  CONCLUSIONS
  When using overlapping peptides to screen for CD8 T cell responses, more sensitive detection will be achieved using known C-terminal anchor amino acid residues at the C-terminus.
authors.affiliation: Howard Hughes Medical Institute and Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School Division of AIDS, Boston, MA, USA.
authors.forename: Rika
authors.initials: R
authors.lastname: Draenert
authors.forename: Christian
authors.initials: C
authors.lastname: Brander
authors.forename: Xu G
authors.initials: XG
authors.lastname: Yu
authors.forename: Marcus
authors.initials: M
authors.lastname: Altfeld
authors.forename: Cori L
authors.initials: CL
authors.lastname: Verrill
authors.forename: Margeret E
authors.initials: ME
authors.lastname: Feeney
authors.forename: Bruce D
authors.initials: BD
authors.lastname: Walker
authors.forename: Philip J R
authors.initials: PJ
authors.lastname: Goulder
mesh_terms: D020816:Amino Acid Motifs; D000937:Antigen-Antibody Reactions; D000956:Antigens, Viral / Q000235:genetics*; D018414:CD8-Positive T-Lymphocytes / Q000276:immunology*; D003601:Cytotoxicity Tests, Immunologic; D000939:Epitopes / Q000235:genetics*; D006801:Humans
chemical_list: D000956:Antigens, Viral; D000939:Epitopes