Sequence conservation of subdominant HLA‐A2‐binding CTL epitopes in HIV‐1 clinical isolates and CD8⁺ T‐lymphocyte cross‐recognition may explain the immune reaction in infected individuals

Abstract

Cytotoxic T-lymphocytes (CTL) are critical for immune control of infection with human immunodeficiency virus type-1 (HIV-1) and searches for relevant CTL epitopes for immune therapy are ongoing. Recently, we identified 28 HLA-A2-binding HIV-1 CTL epitopes (1). In this follow-up study we fully genome sequenced HIV-1 from 11 HLA-A2(+) patients to examine the sequence variation of these natural epitopes and compared them with the patient's CD8(+) T-cell recall response. Often the epitope was conserved but only a few patients showed a CD8(+) T-cell recall response. This infrequent targeting may be explained by immune subdominance. CD8(+) T-cell recall response to a natural epitope could be measured despite sequence differences in the patient's virus. T-cell cross-reaction between such variants could be demonstrated in HLA-A2 transgenic mice. Nine infrequently targeted but conserved or cross-reacting epitopes were identified in seven HIV-1 proteins. More immunogenic anchor amino acid optimized immunogens were designed that induced T-cell cross-reaction with these natural epitopes. It is concluded that most of the new CTL epitopes are conserved but subdominant during the infection. It is suggested that T-cell promiscuity may explain the observed CD8(+) T-cell reaction to epitope variants and it may be possible to use the selected immune optimized epitope peptides for therapeutic vaccination.

Induction of novel CD8+ T-cell responses during chronic untreated HIV-1 infection by immunization with subdominant cytotoxic T-lymphocyte epitopes

“…Sequencing plasma HIV-1 RNA confirmed that in all individuals the majority of the epitopes or epitope variants previously shown to cross-react in HLA-A Ã 0201 mice [14] were present before immunization (Table 1). We followed plasma HIV-1 viral load and CD4 þ T-cell counts for 1 year prior to and up to 8 months after the dendritic cell immunization (Fig.…”

“…We tested the immunogenicity of the selected peptides in HLA-A Ã 0201 transgenic mice and confirmed their infrequent targeting but in-vivo processing in untreated HIV-1-infected individuals [13,14]. To compensate for the high diversity of HIV-1 and investigate the potential for targeting the virus at several different highly conserved regions simultaneously [15], we selected seven of these novel HLA-A2 CTL epitopes derived from several proteins in HIV-1 [14,16]. Weak immunogenic target epitopes were modified into potent peptide immunogens by anchor optimization and confirmed improved immunogenicity and cross-reaction to the target epitopes [13,14].…”

“…Peptides were suspended at 1 mg/ml in clinical grade Roswell Park Memorial Institute (RPMI) media, filtered through a 0.22 mm filter and tested for sterility and endotoxins. To improve immunogenicity of selected subdominant epitopes, we used primary anchor optimized variants with improved binding to HLA-A Ã 0201 [14]. One minimal 8mer epitope (Gag433) was not optimized, as the HLA-A Ã 0201 binding and immunogenicity was already acceptable.…”

“…To identify subdominant and conserved CTL epitope targets, we used 'reverse immunology' through computerized artificial neural network predictions of HLA-A Ã 0201 binding, followed by measurement of actual peptide binding in vitro [13]. We tested the immunogenicity of the selected peptides in HLA-A Ã 0201 transgenic mice and confirmed their infrequent targeting but in-vivo processing in untreated HIV-1-infected individuals [13,14]. To compensate for the high diversity of HIV-1 and investigate the potential for targeting the virus at several different highly conserved regions simultaneously [15], we selected seven of these novel HLA-A2 CTL epitopes derived from several proteins in HIV-1 [14,16].…”

“…To compensate for the high diversity of HIV-1 and investigate the potential for targeting the virus at several different highly conserved regions simultaneously [15], we selected seven of these novel HLA-A2 CTL epitopes derived from several proteins in HIV-1 [14,16]. Weak immunogenic target epitopes were modified into potent peptide immunogens by anchor optimization and confirmed improved immunogenicity and cross-reaction to the target epitopes [13,14]. CD4 þ T-cell help is needed for induction of new CD8 þ T-cell immunity.…”