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* Division of Infectious Diseases and Immunology and Cooperative Research Center for Vaccine Technology, Queensland Institute of Medical Research, and Department of Molecular and Cellular Pathology, University of Queensland, Brisbane, Australia;
Department of Histology, Faculty of Medicine, Gadjah Mada University, Yogyakarta, Indonesia; and
Molecular Genetics Laboratory, Tissue Typing Services, Australian Red Cross Blood Service, Sydney, Australia
| Abstract |
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| Introduction |
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More recent studies have demonstrated a degree of degeneracy in HLA-peptide binding, whereby multiple class I alleles can recognize common sequence motifs (referred to as supermotifs) due to homology of amino acids within the major binding pockets of the peptide binding cleft, and these groups of alleles are referred to as HLA supertypes. Based on these HLA structural similarities and overlapping peptide binding motifs, nine major HLA supertypes have been proposed (8). For example, the A2 supertype includes HLA A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*6802, and A*6901 (9). These alleles recognize peptides with small or aliphatic hydrophobic residues (L, I, V, M, A, T, or Q) at position 2 and L, I, V, M, A, or T at the C-terminal position. The biological significance of several HLA supertypes has also been demonstrated, with reports of individual peptides binding to multiple HLA alleles and T cell recognition of such peptides presented by the different class I alleles (10, 11, 12, 13, 14, 15, 16, 17). The HLA-A24-supertype was proposed in 1999 by Sette and Sidney (8) to include A*2301, A*2402, and A*3001 on the basis of similarities between the published peptide binding motifs for A*2402 (18, 19) and A*3001 (20) and homology with two peptides known to bind to A*2301 (21, 22). The alleles A*2403, A*2404, A*3002, and A*3003 were also tentatively included within the A24 supertype on the basis of possessing identical or conservatively similar amino acid residues surrounding the likely B- and F-pockets in these alleles compared with A*2301, A*2402, and A*3001. Thus, an A24 supermotif was proposed to include Y or F (or, less frequently, W, L, V, I, M, or T) at peptide position 2 and F or I (or, less frequently, Y, W, L, or M) at the C terminus. No further evidence in support of this proposed A24 supertype has been published to date. The A24 supertype is highly represented in different ethnic groups, such as Caucasians (23.9%), Chinese (40.1%), and Japanese (58.6%) (8). Therefore, biological validation of this supertype and identification of antigenic peptides from viral Ags with the capacity to bind promiscuously across the supertype could promote efforts to develop epitope-based vaccines or immunotherapy. The present report has addressed this issue by examining two viral epitopes (from EBV and CMV) initially identified as HLA-A*2301-binding peptides. The data clearly demonstrate that these peptides are recognized by T cells in association with different alleles of the A24 supertype, and in the case of the EBV peptide, CTL responses are directed toward this single epitope in both A*2301+ and A*2402+ individuals. CTL clones were isolated with promiscuous HLA restriction, displaying a capacity to recognize the peptides in association with HLA A*2301 or A*2402. Together these data confirm the immunological relevance of grouping at least these three alleles within an A24 supertype.
| Materials and Methods |
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Lymphoblastoid cell lines (LCLs)4 were established by exogenous transformation of peripheral B cells with EBV derived from the supernatant of the B95.8 cell line and were maintained in growth medium (10% FCS/RPMI 1640). Some HLA-typed LCLs were also obtained from the European Collection of Cell Cultures. PHA blasts were generated by stimulating PBMCs with PHA (Sigma-Aldrich, Sydney, Australia), and after 3 days, growth medium containing supernatant from the MLA-144 cell line (American Type Culture Collection, Manassas, VA) and rIL-2 was added. PHA blasts were propagated with biweekly replacement of rIL-2 and MLA-144 supernatant (PHA free) for up to 8 wk. The blood donors used in this study were healthy laboratory staff selected for particular HLA alleles and prior exposure to either EBV or CMV as assessed by standard virus-specific Ab tests. All cell lines were regularly screened for mycoplasma contamination.
CTL clones were generated by agar cloning as follows. PBMCs (2 x 106) were stimulated in 2 ml of growth medium with autologous cells presenting a viral epitope. These stimulator cells were either PBMCs precoated with the CMV peptide AYAQKIFKIL (1 µM for 1 h, responder/stimulator ratio of 2:1) or gamma-irradiated (8000 rad) LCLs (responder/stimulator ratio of 50:1) to raise clones against the EBV peptide PYLFWLAAI. After 3 days, cells were dispersed and seeded in 0.35% agarose (Seaplaque; BioWhittaker Molecular Applications, Rockland, ME) containing RPMI 1640, 20% FCS, 25% supernatant from MLA-144 cultures, and rIL-2 (50 U/ml). Colonies were harvested after a further 35 days and were amplified in culture with biweekly restimulation with rIL-2, MLA-144 supernatant, and the gamma-irradiated (8000 rad) autologous LCL. These LCL stimulators were prelabeled with the CMV peptide AYAQKIFKIL for use with clones initially raised against this peptide. CTL clone CSIC7 has been described previously (21).
Short term CTL microcultures were generated by limiting dilution as follows. PBMCs were distributed in round-bottom microtiter plates in growth medium at cell numbers ranging from 103 to 5 x 104 cells/well. Approximately 5 x 104 gamma-irradiated (2000 rad) autologous PBMCs that had been preincubated with the EBV peptide PYLFWLAAI (1 µM for 1 h), were added to each well to give a total volume of 100 µl. Cultures were fed on days 4 and 7 with 50 µl of medium supplemented with 20 U of rIL-2 and 25% (v/v) supernatant from MLA-144 cultures. On day 10, each CTL microculture was split into four replicates and used as effectors in a standard 5-h 51Cr release assay against target PHA blasts (HLA A*2402+ or A*2301+) that had been treated with peptide PYLFWLAAI or left untreated. The data shown in Figs. 2 and 3A were from CTL microcultures raised from responder PBMC concentrations from which less than half the wells produced CTLs specific for the EBV epitope; thus, most were likely to have been generated from a single PYLFWLAAI-specific CTL.
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CTL clones were tested in duplicate for cytotoxicity in the standard 5-h chromium release assay. Briefly, CTLs were assayed against 51Cr-labeled LCL or PHA blast targets that were pretreated with synthetic peptide and washed or were left untreated. Peptides were synthesized by Mimotopes (Clayton, Australia). Toxicity testing of all peptides was performed before use by adding peptide to 51Cr-labeled PHA blasts in the absence of CTL effectors. In some experiments target cells were infected with recombinant vaccinia virus at a multiplicity of infection of 10:1 for 1 h at 37°C. After overnight infection, cells were washed with growth medium, incubated with 51Cr for 60 min, and used as targets in a 51Cr release assay. Recombinant vaccinia virus constructs encoding the latent membrane protein 2A (LMP2A) Ag of EBV (Vacc.LMP2A), the IE1 Ag of CMV (Vacc IE1), and a vaccinia virus construct made by insertion of the pSC11 vector alone and negative for thymidine kinase (Vacc.TK-) have been previously described (23, 24). A beta scintillation counter (Topcount Microplate; Packard Instrument, Meriden, CT) was used to measure 51Cr levels in assay supernatant samples. The mean spontaneous lysis for target cells in culture medium was always <20%, and the variation about the mean specific lysis was <10%.
| Results |
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ELISPOT assays, a 10-aa peptide (AYAQKIFKIL) from the IE1 Ag was identified as an immunogenic sequence in two HLA A*2301+, CMV-exposed individuals (data not shown). CTL clones were raised from each of these individuals against the AYAQKIFKIL peptide and screened for cross-recognition of the peptide on a range of HLA-mismatched LCLs, as was done with the EBV-specific CTL clone. The data shown in Fig. 1B are for clone JW29.2, and very similar results were obtained with the second clone (data not shown). As with the EBV-specific CTLs, these CMV-specific T cells exhibited promiscuous HLA restriction, recognizing the AYAQKIFKIL peptide in association with either self-HLA-A*2301, or the non-self-HLA A*2402. No lysis was observed through other HLA alleles, such as A*2403 or A*3003, although peptide-pulsed target cells expressing A*3002 were recognized at low levels by the clones.
Since the promiscuous HLA restriction observed with EBV-specific CTLs was demonstrated with only one clone, experiments were conducted to determine how frequently this pattern of cross-reactivity is displayed. CTL microcultures were raised at limiting dilution against the PYLFWLAAI peptide by stimulating PBMCs from an HLA A23+, EBV-sero+ individual with the peptide. All CTL cultures reactive toward the EBV peptide were capable of recognizing the peptide in the context of self-HLA-A*2301 or non-self-HLA-A*2402 (Fig. 2), indicating that these two peptide-HLA complexes share considerable structural similarity. Notably, HLA A*2301 and A*2402 differ by just four amino acids, and two of these differences are located at positions unlikely to influence either peptide binding or TCR interactions. However, the conserved mismatch at amino acid position 151 (Arg in A*2301 and His in A*2402), which is located at the docking surface of the HLA has the potential to influence TCR interactions. Furthermore, the mismatch at the
2 helix position 156 (Leu in A*2301 and Gln in A*2402), which projects into the peptide binding groove, could theoretically influence peptide binding or conformation (26).
These data demonstrate indirectly that the PYLFWLAAI epitope binds to multiple alleles of the A24 supertype, raising the possibility that this peptide is immunogenic in individuals expressing the common A*2402 subtype. To investigate whether A*2402+ people respond to EBV infection with a T cell response to this LMP2A epitope, CTL microcultures were raised, as described above, from virus-exposed donors expressing this HLA allele. Representative data for eight CTL microcultures from four different donors, shown in Fig. 3A, clearly demonstrate that A*2402+ individuals do respond this epitope. Interestingly, seven of the eight CTL cultures also showed cross-recognition of the peptide in association with A*2301. A PYLFWLAAI-specific CTL clone (AM9) from an EBV-exposed individual expressing both A*2402 and A*2407 was then raised and tested against a large panel of target cells, with and without peptide pretreatment, and again degeneracy in HLA restriction was observed (Fig. 3B). The clone recognized the peptide in association with A*2301, A*2402, or A*2403.
Two CMV-sero+ donors who expressed HLA A*2402 were also tested for CTL responses to the AYAQKIFKIL peptide using the IFN-
ELISPOT assay; however, no responses were detected, suggesting that this peptide is nonimmunogenic in A*2402+ individuals (data not shown). It was not possible to assess CTL responses to these EBV and CMV epitopes in A*3001+ individuals because donors expressing this HLA allele were unavailable for this study.
To determine whether these CTL clones raised from A*2301+ and A*2402+ individuals displayed degeneracy in HLA restriction against target cells presenting endogenously processed viral peptide, target cells were infected with recombinant vaccinia virus constructs encoding the LMP2A Ag of EBV, the IE1 Ag of CMV, or a vaccinia virus construct made by insertion of the pSC11 vector alone and negative for thymidine kinase (Vacc.TK-). As shown in Fig. 4A, the A*2301+ CTL clone CSIC7 displayed classical self-HLA-restriction when the target EBV peptide was processed endogenously. In contrast, the EBV-specific AM9 CTL clone cross-recognized the LMP2A Ag expressed in A*2402+ or A*2301+ target cells (Fig. 4B). Furthermore, the A*2301+ CMV-specific CTL clone JW29.2 demonstrated a capacity to kill IE1-expressing cells with this same subset of HLA A24-supertype alleles (Fig. 4C).
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| Discussion |
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The broad immunogenicity of the PYLFWLAAI epitope has potentially important practical implications for EBV vaccine development. The LMP2A Ag of EBV is of particular interest in this context because it is one of the few EBV Ags expressed in malignancies such as nasopharyngeal carcinoma and Hodgkins disease (27). Since it is well established that immunization with whole viral proteins does not elicit an efficient CTL response, interest has been directed toward epitope-based vaccines, particularly with oncogenic viruses such as EBV, in which individual viral genes have the potential to initiate tumorigenic processes. A major potential obstacle to developing such vaccines is the large number of epitopes potentially required to achieve broad population coverage, given the extreme degree of polymorphism in HLAs. Before this investigation, the PYLFWLAAI epitope was thought to be immunogenic in only HLA A*2301+ individuals, an HLA allele with a gene frequency of only 1.3% of Caucasians and 0.6% of Asians (28). Our data demonstrate that this peptide also stimulates a CTL response through the much more common allele A*2402 (gene frequency of 6.6% in Caucasians and 18.9% in Asians). This study has therefore highlighted a much broader potential population coverage of this single LMP2A epitope if included in a CTL-based EBV vaccine.
The cross-reactivity of the AM9 CTL clone with the EBV peptide presented at very limiting concentrations on A*2301 or A*2402, shown clearly in Fig. 5B, suggests exceptional degeneracy at the level of both peptide binding and TCR recognition. The mechanism by which the TCR expressed by AM9 tolerates these major differences will only be determined by crystal structure analysis, but presumably it can be triggered by these distinct complexes without making major contacts with the side chains of these divergent
helix residues. It is relevant to point out that the AM9 CTL clone was raised from an Indonesian donor who expressed both A*2402 and the rare allele A*2407. It is possible that broadly reactive CTLs have been preferentially selected in this donor for their capacity to cross-recognize the EBV peptide in association with each of these alleles. It is also notable that human CTL clones raised against foreign peptides often display cross-reactivity with alloantigens and are therefore tolerant of amino acid differences between the selecting self-HLA allele and the allo-HLA target Ag (29, 30, 31, 32, 33).
Degenerate peptide binding to multiple HLA alleles that are grouped together as an HLA supertype is now a widely accepted phenomenon, and this report has confirmed the validity of the A24 supertype. It is probably less well excepted that, as a consequence of this degeneracy in peptide binding, along with additional degeneracy at the level of TCR recognition, T lymphocytes with 
TCRs are not always self-MHC restricted. The dogma that defines recognition of foreign peptides by 
T cells is that it only occurs in the context of a presenting self-MHC protein. Clones such as AM9 can clearly recognize the same foreign peptide with similar efficiency in association with a self-HLA or some non-self-HLAs. Several other examples of CTL clones with very promiscuous HLA restriction have been described in which the degeneracy is observed with low concentrations of exogenous peptide or after endogenous peptide processing (13, 15, 16). The interaction between a TCR and an MHC occurs within a limited area on the top surface of the MHC molecule and, as illustrated with the AM9 CTL clone, 
TCRs can accommodate a degree of polymorphism in the exposed
helix residues between the restricting MHC and foreign MHC Ags that present the same peptide. Self-MHC restriction is controlled at the level of both peptide-MHC and TCR-MHC binding, and since MHC molecules differ primarily in amino acids that bind peptide rather than at positions predicted to be directly accessible to TCRs (34), the specificity of peptide binding is likely to be the more important factor. Despite this polymorphism, peptides do commonly bind to multiple MHC Ags, and it is therefore likely that a significant proportion of 
T cells can recognize foreign peptides on self- and non-self MHC Ags and are therefore not strictly self-MHC restricted.
| Acknowledgments |
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| Footnotes |
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2 S.R.B. and R.A.E. contributed equally to this work. ![]()
3 Address correspondence and reprint requests to Dr. Scott R. Burrows, Cellular Immunology Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane 4029, Australia. E-mail address: scottb{at}qimr.edu.au ![]()
4 Abbreviations used in this paper: LCL, lymphoblastoid cell line; LMP2A, latent membrane protein 2A. ![]()
Received for publication January 27, 2003. Accepted for publication May 13, 2003.
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