title: Multiple T-cell epitopes overlap positively-selected residues in the p1 spacer protein of HIV-1 gag.
abstract: OBJECTIVE
  The p1 region of HIV-1 gag contains the frameshift stem-loop, gag-pol transframe and a protease cleavage site that are crucial for viral assembly, replication and infectivity. Identifying and characterizing CD8+ epitopes that are under host immune selection in this region will help in designing effective vaccines for HIV-1.
  
  
  METHODS
  An approach combining bioinformatical analysis and interferon gamma enzyme-linked immunosorbent spot (ELISPOT) assays is used to identify and characterize the epitopes. Potential human leukocyte antigen (HLA)-restricted epitopes were identified by correlating the positively-selected mutations with host HLA alleles.
  
  
  METHODS
  ELISPOT analysis with overlapping peptides was used to confirm and characterize the epitopes.
  
  
  RESULTS
  Four positively-selected residues were significantly associated with HLA class I alleles, including HLA B*1302 (K4R, P = 0.0008 and I5L, P = 0.0108), A*7401 (S9N, P = 0.0002) and A*30 genotypes (P7S, P = 0.009), suggesting epitopes restricted by these alleles are present in this region. ELISPOT analysis with patient peripheral blood mononuclear cells (PBMCs) identified seven novel epitopes restricted by the 3 alleles. Two types of epitopes were observed in this region based on the ELISPOT responses, Type I: the positively-selected variation does not affect CD8+ T-cell responses; and Type II: the CD8+ T-cell responses are determined by the epitope variants.
  
  
  CONCLUSIONS
  We identified and characterized seven novel CD8+ epitopes in the p1 spacer protein region. Classifying the effects of positively-selected variants on CD8+ T-cell responses will help in designing effective vaccines for HIV-1.
authors.affiliation: Department of Medical Microbiology, University of Manitoba, National Microbiology Laboratory, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada. ma_luo@phac-aspc.gc.ca
authors.forename: Christina A
authors.initials: CA
authors.lastname: Semeniuk
authors.forename: Lyle
authors.initials: L
authors.lastname: McKinnon
authors.forename: Harold O
authors.initials: HO
authors.lastname: Peters
authors.forename: Michael
authors.initials: M
authors.lastname: Gubbins
authors.forename: Xiaojuan
authors.initials: X
authors.lastname: Mao
authors.forename: Terry B
authors.initials: TB
authors.lastname: Ball
authors.forename: Ma
authors.initials: M
authors.lastname: Luo
authors.forename: Francis A
authors.initials: FA
authors.lastname: Plummer
mesh_terms: D000483:Alleles; D018414:CD8-Positive T-Lymphocytes / Q000276:immunology*; D002478:Cells, Cultured; D018984:Epitopes, T-Lymphocyte / Q000235:genetics / Q000276:immunology*; D005260:Female; D015683:Gene Products, gag / Q000235:genetics / Q000276:immunology*; D015658:HIV Infections / Q000235:genetics / Q000276:immunology*; D015497:HIV-1 / Q000276:immunology*; D006680:HLA Antigens / Q000235:genetics / Q000276:immunology; D006801:Humans; D007150:Immunohistochemistry; D010455:Peptides / Q000235:genetics / Q000276:immunology; D012367:RNA, Viral / Q000235:genetics / Q000276:immunology
chemical_list: D018984:Epitopes, T-Lymphocyte; D015683:Gene Products, gag; D006680:HLA Antigens; D010455:Peptides; D012367:RNA, Viral