title: Identification of subdominant cytotoxic T lymphocyte epitopes encoded by autologous HIV type 1 sequences, using dendritic cell stimulation and computer-driven algorithm.
abstract: Conventional analysis of the cytotoxic T lymphocyte (CTL) response to HIV-1 may underestimate the true breadth of CTL epitopes recognized. This underestimation could be due to several reasons, including (1) the use of laboratory-adapted stains of HIV or consensus sequences, which would lead to the identification of only highly conserved epitopes, (2) the use of EBV-transformed B cells (B-LCLs) and vaccinia virus constructs in standard assays that may obscure low level CTL responses due to high EBV or vaccinia reactivity, and (3) relatively insensitive assays wherein PBMCs instead of professional APCs are used to stimulate CTL responses. To address these problems, we first identified an immunodominant HLA-B7-restricted CTL epitope, by standard cloning methods, in a long-term nonprogressor (LTNP). To determine whether the patient had CTLs specific for autologous viral sequences other than the dominant epitope, proviral DNA was cloned and sequenced. A matrix-based epitope algorithm (EpiMatrix) was used to identify the top 2% of peptides from the viral sequences with the highest likelihood of binding to HLA-B7. These 55 peptides were synthesized and tested for HLA-B7 binding in a T2/B7 cell line; 10 peptides were able to stabilize HLA-B7 on the cell surface. By using peptide-pulsed autologous dendritic cells as a more sensitive method of CTL stimulation, we found three additional subdominant CTL epitopes.
authors.affiliation: Aaron Diamond AIDS Research Center, Rockefeller University, New York, New York 10016, USA. xjin@adarc.org
authors.forename: X
authors.initials: X
authors.lastname: Jin
authors.forename: C G
authors.initials: CG
authors.lastname: Roberts
authors.forename: D F
authors.initials: DF
authors.lastname: Nixon
authors.forename: J T
authors.initials: JT
authors.lastname: Safrit
authors.forename: L Q
authors.initials: LQ
authors.lastname: Zhang
authors.forename: Y X
authors.initials: YX
authors.lastname: Huang
authors.forename: N
authors.initials: N
authors.lastname: Bhardwaj
authors.forename: B
authors.initials: B
authors.lastname: Jesdale
authors.forename: A S
authors.initials: AS
authors.lastname: DeGroot
authors.forename: R A
authors.initials: RA
authors.lastname: Koup
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D003713:Dendritic Cells / Q000276:immunology*; D018984:Epitopes, T-Lymphocyte / Q000032:analysis* / Q000276:immunology; D015683:Gene Products, gag / Q000276:immunology; D015658:HIV Infections / Q000276:immunology* / Q000821:virology; D015497:HIV-1 / Q000235:genetics / Q000276:immunology*; D015793:HLA-B7 Antigen / Q000276:immunology; D006801:Humans; D016056:Immunodominant Epitopes / Q000032:analysis* / Q000276:immunology; D013602:T-Lymphocytes, Cytotoxic / Q000276:immunology*
chemical_list: D018984:Epitopes, T-Lymphocyte; D015683:Gene Products, gag; D015793:HLA-B7 Antigen; D016056:Immunodominant Epitopes