The Journal of Immunology, 2004, 173: 2895.
Copyright © 2004 by The American Association of Immunologists
Predictive Algorithms and T Cell Epitope Mapping
Rajiv Khanna
Tumor Immunology Laboratory, Division of Infectious Diseases and Immunology, Queensland Institute of Medical Research, Brisbane, Australia
In a recent paper, Pelte et al. (1) used predictive algorithms (2, 3) and ex vivo T cell assays to map potential epitopes from HCMV. Of the 261 peptides tested, only one peptide stimulated T cells that failed to stabilize HLA-A2 expression on T2 cells. Pelte et al. concluded that this epitope is unlikely to be HLA-A2 restricted and raised concerns on the HLA restriction of some of the previously published HCMV T cell epitopes by our group (4). While using predictive algorithms and MHC stabilization assays, one has to very careful to understand the limitations of these procedures. Based on our extensive experience with three different viruses (HCMV, EBV, and HCV; Refs.4, 5, 6), we have found that there is never a perfect correlation between the predictive scores, HLA stabilization on T2 cells, and ex vivo T cell stimulation assays (see Fig. 1). Occasionally, peptides that poorly stabilize HLA-A2 can be confirmed as CD8+ T cell epitopes. Indeed, despite poor HLA stabilization by the peptide AVGGAVASV, we were able to expand T cells that recognized epitope-sensitized HLA-A2-positive target cells (4). We are now testing other peptides (US2 and gH) to see whether specific CTLs can be expanded from humans and HLA-A2/Kb mice. Furthermore, if a T cell response cannot be detected using ex vivo assays, it should not be assumed that the Ags from which these peptides were derived do not include T cell epitopes. This may be due to very low precursor frequencies or the limitations in the ex vivo functional assays. For example, using pooled peptides (especially when all peptides are potentially restricted through the same HLA allele) in any ex vivo assay can significantly compromise the readout due to competition between the peptides within an individual pool.
References
- Pelte, C., G. Cherepnev, Y. Wang, C. Schoenemann, H.-D. Volk, F. Kern. 2004. Random screening of proteins for HLA-A*0201-binding nine-amino acid peptides is not sufficient for identifying CD8 T cell epitopes recognized in the context of HLA- A*0201. J. Immunol. 172:6783.[Abstract/Free Full Text]
- Rammensee, H. G., J. Bachmann, S. Stefanovic. 1997. MHC Ligands and Motifs Landes Bioscience, Georgetown.
- Parker, K. C., M. A. Bednarek, J. E. Coligan. 1994. Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J. Immunol. 152:163.[Abstract]
- Elkington, R., S. Walker, T. Crough, M. Menzies, J. Tellam, M. Bharadwaj, R. Khanna. 2003. Ex vivo profiling of CD8+ T cell responses to human cytomegalovirus reveals broad and multispecific reactivities in healthy virus carriers. J. Virol. 77:5226.[Abstract/Free Full Text]
- Khanna, R., S. R. Burrows, J. Nicholls, L. Poulsen. 1998. Identification of cytotoxic T cell epitopes within Epstein-Barr virus (EBV) oncogene latent membrane protein 1 (LMP1): evidence for HLA A2 supertype restricted immune recognition of EBV-infected cells by LMP1-specific cytotoxic T lymphocytes. Eur. J. Immunol. 28:451.[Medline]
- Khanna, R., M. Sherritt, S. R. Burrows. 1999. EBV structural antigens, gp350 and gp85, as targets for ex vivo virus-specific CTL during acute infectious mononucleosis: potential use of gp350/gp85 CTL epitopes for vaccine design. J. Immunol. 162:3063.[Abstract/Free Full Text]
, Peptide epitopes showing T cell reactivity in ELISPOT and/or CTL assays; 
, peptides showing no detectable T cell reactivity. The dotted line indicates the mean ± 3 SEM of the fluorescence intensity for HLA-A2 on T2 cells incubated at 26°C without peptide, which was the cutoff for a positive HLA-A2 stabilization. Each symbol on the graph represents an individual predicted peptide epitope. This analysis is based on >70 different predicted HLA-A2-restricted epitopes.