Identification of Seventeen New Simian Immunodeficiency Virus-Derived CD8+ T Cell Epitopes Restricted by the High Frequency Molecule, Mamu-A*02, and Potential Escape from CTL Recognition

Abstract

MHC class I-restricted CD8+ T cells play an important role in controlling HIV and SIV replication. In SIV-infected Indian rhesus macaques (Macaca mulatta), comprehensive CD8+ T cell epitope identification has only been undertaken for two alleles, Mamu-A*01 and Mamu-B*17. As a result, these two molecules account for virtually all known MHC class I-restricted SIV-derived CD8+ T cell epitopes. SIV pathogenesis research and vaccine testing have intensified the demand for epitopes restricted by additional MHC class I alleles due to the shortage of Mamu-A*01+ animals. Mamu-A*02 is a high frequency allele present in over 20% of macaques. In this study, we characterized the peptide binding of Mamu-A*02 using a panel of single amino acid substitution analogues and a library of 497 unrelated peptides. Of 230 SIVmac239 peptides that fit the Mamu-A*02 peptide-binding motif, 75 peptides bound Mamu-A*02 with IC50 values of ≤500 nM. We assessed the antigenicity of these 75 peptides using an IFN-γ ELISPOT assay with freshly isolated PBMC from eight Mamu-A*02+ SIV-infected macaques and identified 17 new epitopes for Mamu-A*02. The synthesis of five Mamu-A*02 tetramers demonstrated the discrepancy between tetramer binding and IFN-γ secretion by SIV-specific CD8+ T cells during chronic SIV infection. Bulk sequencing determined that 2 of the 17 epitopes accumulated amino acid replacements in SIV-infected macaques by the chronic phase of infection, suggestive of CD8+ T cell escape in vivo. This work enhances the use of the SIV-infected macaque model for HIV and increases our understanding of the breadth of CD8+ T cell responses in SIV infection.

In vivoCD8+T cell control of immunodeficiency virus infection in humans and macaques

“…Indeed, in humans, protective alleles appear to be associated with decreased frequency of escape (22). There is no evidence that humans have broader CTL responses (i.e., recognize more epitopes) than macaques (24)(25)(26)(27)(28)(29), so, given the observation that individual CTL responses kill virus-infected cells more rapidly in macaques than in humans, we conclude that the total CTL response kills immunodeficiency virus-infected cells more rapidly in macaques than in humans. Our work does not enable us to determine whether CD8 ϩ T cells from macaques kill at a faster rate because there are more CD8 ϩ T cells targeting each peptide or because the per-CD8 ϩ T cell rate of killing is higher.…”

Unusually High Frequency MHC Class I Alleles in Mauritian Origin Cynomolgus Macaques

“…In these studies, the peptide binding motif for an allele is determined; the SIV proteome is scanned for peptides that fit the motif; the peptides are experimentally tested for binding affinity; and peptides that exceed the binding threshold are tested for antigenicity in SIV-infected animals. For each allele, at least five SIVspecific CD8 ϩ T lymphocyte responses were identified (41,71,72). Therefore, it is reasonable to forecast that at least one (and perhaps all) of the three common MHC I alleles identified in Mauritian Cynomolgus macaques will restrict SIV-specific CD8 ϩ T lymphocyte responses.…”

Mhc class I haplotypes associated with survival time in simian immunodeficiency virus (SIV)-infected rhesus macaques

“…Mamu-A*02 presents an epitope from each of Nef 32 and Gag in a dominant fashion, and several other epitopes subdominantly. 33 The estimated mean survival time of six monkeys from five independent breeding groups was 31.3 w.p.i., which represents an underestimate because the largest observation was censored. Nevertheless, the presence of Mamu-A*02 significantly prolonged survival in the respective animals (logrank w 2 ¼ 7.426, one d.f., P ¼ 0.006).…”