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Journal of Virology, July 2006, p. 6318-6323, Vol. 80, No. 13
0022-538X/06/$08.00+0 doi:10.1128/JVI.00427-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Isaac G. Sakala,3
John Sidney,4
Alessandro Sette,4
Denis J. Moss,2
Jack R. Bennink,1
Gunasegaran Karupiah,3 and
Jonathan W. Yewdell1*
Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-0440,1 Division of Immunology and Infectious Diseases, Queensland Institute of Medical Research, Herston QLD 4006, Australia,2 Division of Immunology and Genetics, John Curtin School of Medical Research, Australian National University, Canberra ACT 2601, Australia,3 Division of Translational Immunology and Biodefense, La Jolla Institute for Allergy and Immunology, San Diego, California 921214
Received 28 February 2006/ Accepted 18 April 2006
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Although CD8+ T cells (TCD8+) are important antiviral effectors in poxvirus immunity (13), studies of TCD8+ responses to poxviruses have been hampered by the absence of information regarding the peptide determinants they recognize. The initial TCD8+ determinants recognized in the context of Kb and Db were described recently (18, 26). Given the influence of major histocompatibility complex (MHC) and non-MHC genes on pathogenicity of poxviruses (3), it is important to study immunity to poxviruses in a variety of mouse strains. BALB/c mice have been widely used as a model for studying VACV immunology (1, 10, 30, 32) and pathogenesis, especially by the intranasal route (27, 28, 31).
Here we define the initial TCD8+ determinants for VACV in H-2d-haplotype mice and explore cross-reactivity of TCD8+ specific for these peptides with natural variants found in other orthopoxviruses, including cowpox virus (CPXV) and ectromelia virus (ECTV), the causative agent of mousepox.
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Synthetic peptides. Peptides were synthesized by A & A Labs (San Diego, CA) at the John Curtin School of Medical Research Biomolecular Resources Facility or purchased as crude material from Mimotopes (Minneapolis, MN) or Pepscan Systems B.V. (Lelystad, The Netherlands). Peptides were resuspended at 4 to 20 mg/ml in 100% dimethyl sulfoxide and then diluted to required concentrations in PBS, PBS with 0.05% NP-40, or RPMI 1640. Peptides for use as probes were radiolabeled using the chloramine T method (22) after purification to >95% by reverse-phase high-pressure liquid chromatography.
Mice, infections, and immunizations. Specific-pathogen-free BALB/c mice were obtained from Taconic (Gaithersburg, MD), Animal Resource Centre (Perth, Australia), or Animal Services Division, John Curtin School of Medical Research. Mice were housed and experiments done in accordance with relevant ethics requirements. In all VACV experiments, mice were infected intraperitoneally (i.p.) and doses ranged from 5 x 104 to 1 x 106 PFU/mouse for WR and 5 x 107 to 1 x 108 PFU/mouse for MVA. Mice were also infected with CPXV i.p., using a dose of 1 x 105 PFU. ECTV-TK infections were done subcutaneously (s.c.) in the shank, using 2 x 107 PFU. A TK mutant was chosen for these experiments, because fully virulent ECTV is lethal in BALB/c mice at any infective dose. The s.c. route was used, since ECTV is thought to be transmitted by a peripheral route and pathogenesis after i.p. infection is thought to be less true to the natural infection (8, 17).
Generation of 293 cells expressing mouse MHC genes. The complete coding sequences for H-2Kd (Kd), H-2Dd (Dd), and H-2Ld (Ld) were amplified by PCR from recombinant VACV encoding these products and cloned into pcDNA3.1D/V5-His-TOPO (Invitrogen). Primers used were as follows: Kd, CACCATGGCACCCTGCACGC and TCACGCTAGAGAATGAGGGTC; Dd, CACCATGGGGGCGATGGCTC and TCACACTTTACAATCTGGGAGAGAC; Ld, CACCATGGGGGCGATGGCTC and TCACGCTTTACAATCTCGGA. All clones were verified by sequencing and comparison to GenBank entries: Kd, U47329; Dd, U47326; Ld, M33151. To make stable cell lines, clones were cleaved with SmaI and transfected into 293A cells using Lipofectamine 2000 reagent (Invitrogen). After overnight incubation (37°C, 9% CO2), cells were harvested and six serial 1:5 dilutions made in a fresh six-well plate in medium supplemented with 0.5 mg/ml G418 (Biofluids, MD). Transfectants were cloned by limiting dilution or fluorescence-activated cell sorting (FACS) (based on surface staining for the relevant H-2 product). followed by single-cell deposition (FACStar Plus, BD Biosciences, San Jose, CA) following several weeks of growth in selective medium. Potential H-2-expressing clones were selected by staining with monoclonal antibodies (Pharmingen, BD Biosciences) and analysis on a FACSCalibur instrument (BD biosciences). Clones were maintained in 0.5 mg/ml G418 (but expression of H-2 antigens was found to be stable for several passages in nonselecting medium) and are referred to collectively as 293H-2 cells or individually as 293Kd, 293DdC5, and 293LdA3.
Stimulations and intracellular cytokine staining (ICS).
Whole splenocytes (0.2 x 106 to 1 x 106) or TCD8+ (1 x 105) (CD8a+ T-Cell Isolation kit; Miltenyi Biotec, Aubern, CA) were incubated with (i) transfected cells (26), (ii) peptides, (iii) P815 cells pulsed with peptides, or (iv) P815 cells infected with VACV at 37°C and 5% CO2. Where P815 cells were used as stimulators, they were included at a P815 cell:splenocyte ratio of 1:5. Brefeldin A (10 µg/ml) was added after 1 h, and the incubation was continued for another 3 to 4 h. Cells were then stained with anti-CD8-phycoerythrin (PE) (clone 53-6.7; Pharmingen) (some experiments used fluorescein isothiocyanate or PE-Cy5), washed, fixed with 1% paraformaldehyde, washed, and finally stained with anti-gamma interferon (IFN-
)-allophycocyanin (clone XMG1.2; Pharmingen) (some experiments used fluorescein isothiocyanate or PE) in the presence of 0.5% saponin. A FACSCalibur or FACSCanto instrument (BD Biosciences) was used for acquisition of data, and analysis was done using Flowjo software (Tree Star, Inc., Ashland, OR). Events were gated for live lymphocytes on a forward- and side-scatter gate followed by gating for CD8+ cells using CD8 and side scatter and displayed as CD8 by IFN-
. Backgrounds determined using irrelevant (or no) peptide or uninfected cells were subtracted from test values.
MHC binding assays. Binding of peptides to H-2 allomorphs was determined using quantitative assays based on the inhibition of binding of a radiolabeled standard peptide (22, 26). Briefly, 1 to 10 nM radiolabeled peptide was coincubated at room temperature with 1 µM to 1 nM purified H-2 molecules in the presence of 1 µM human ß2-microglubulin (Scripps Laboratories, San Diego, CA). After a two-day incubation, MHC-peptide complexes were captured on microplates (Greiner Bio-one, Longwood, FL) coated with monoclonal antibody 28-14-8S, SF1-1.1.1, or 34-5-8S for Ld, Kd, or Dd, respectively, and bound radioactivity was measured using a TopCount (Packard Instrument Co.). The concentration of peptide yielding 50% inhibition of the binding of the radiolabeled probe peptide was calculated (IC50).
Sequence comparison. Open reading frame (ORF) and determinant conservation between poxviruses was done with the aid of poxvirus orthologous clusters (29) maintained at the University of Victoria, Victoria, British Columbia, Canada, and accessed through the Poxvirus Bioinformatics Resource (www.poxvirus.org).
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(26). Three immunogenic VACV ORFs were identified, one restricted by each of the three H-2d class I allomorphs (Table 1). Two of the three genes identified encode known VACV immunomodulators, a finding that echoes data from our screen for immunogenic ORFs in C57BL/6 mice (26). A52R encodes an inhibitor of signaling via Toll-like receptors and the interleukin 1 receptor (2), and a VACV lacking this gene is attenuated in mouse models (11). The product of E3L is an inhibitor of the antiviral state induced by interferons (5), and several regions in the E3 protein contribute independently to VACV virulence (14).
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TABLE 1. Immunogenic proteins, TCD8+ determinants, and binding to MHC
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Mapping and characterization of H-2d-restricted VACV TCD8+ determinants.
Immunogenic ORFs were examined for MHC-binding motifs and peptides synthesized for testing in MHC binding and T-cell assays. In each case, the peptide that bound MHC with highest measured affinity was the immunogenic peptide (Table 1). Based on the frequency of responding splenic TCD8+ to primary VACV infection, F226-34 tops the immunodominance hierarchy, followed by A5275-83 and then E3140-148. At
10% of splenic TCD8+ in some mice, the size of responses to F226-34 is among the largest seen for individual determinants in virus infections of mice and comparable to the dominant VACV B820-27 determinant in C57Bl/6 mice (26).
We characterized the potency of synthetic peptides for activating splenic TCD8+ cells from mice infected 7 days previously with VACV (Fig. 1A). All peptides stimulated CD8+ T cells at physiologically relevant peptide concentrations, with half-maximal stimulation being <108 M for each. As an additional test of the validity of the determinants, we determined that peptide-specific TCD8+ lines derived by repeated in vitro stimulation of VACV-immune splenocytes recognized the expected (but not control) VACV gene transfected into 293H-2 cells expressing the appropriate (but not mismatched) restriction element (not shown). These TCD8+ lines also recognized VACV-infected P815 cells (not shown).
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FIG. 1. Characterization of H-2d-restricted VACV TCD8+ determinants. Mice were infected with 106 PFU VACV-WR i.p., and 7 days later, splenocytes were used in ICS assays. (A) Antigenic potency of synthetic peptides. Peptides at the indicated concentrations were used as stimulators for ICS (IFN- ) assays. Data are expressed as percentages of maximum stimulation and are representative of two or more experiments. (B) Anti-TNF and anti-IFN- expression in VACV determinant-specific TCD8+. TNF was used in addition to IFN- in ICS. Plots show CD8+ gated events and are representative of several experiments. Note that TNF+, IFN- events are similar in negative controls and for all VACV peptides.
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in response to each determinant also made TNF; these cells were those that made the largest amounts of IFN-
. The proportion of IFN-
+ cells that also make TNF in responses to VACV-infected P815 cells was similar (not shown). In all cases, the TNF+ population of peptide-specific TCD8+ was entirely contained within the IFN-
+ population, as has been shown previously with mice by use of VACV (using infected cells as stimulators) and other viruses, such as lymphocytic choriomeningitis and influenza A viruses (10, 15, 23). TCD8+ recognizing mapped determinants are a significant proportion of the response to VACV. Next, we determined the fraction of the total TCD8+ response to VACV that is attributable to clones responding to the three determinants. BALB/c mice were infected with VACV, and responses to peptides and VACV-infected P815 cells were measured by ICS (Fig. 2A). Added together, cells recognizing the three determinants account for around 20% of TCD8+ in spleen. In the same experiment, VACV-infected cells were able to stimulate around 45% of splenic TCD8+. This indicates that the mapped determinants account for the specificity of around 40% of the TCD8+ response to acute VACV infection. Similar infections in DBA/2 mice (also H-2d haplotype) gave comparable results (not shown). Determinant-specific TCD8+ were also measured for BALB/c mice infected 12 weeks previously (Fig. 2B), and these data show that for memory responses, while the total size of each response is around eightfold lower, each response contracts proportionally.
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FIG. 2. TCD8+ responses to VACV determinants in the context of the total anti-VACV response. Mice were immunized i.p. with 106 PFU of VACV-WR, and TCD8+ responses of splenocytes were measured by ICS 7 days (A) and 12 weeks (B) later. (Left) Graphs show the percentages of TCD8+ that produce IFN- in ex vivo stimulations with peptides indicated (name of gene shown). (Right) Graphs compare a summation of the peptide data with similar data from the same splenocytes stimulated with VACV-infected P815 cells. Data are means and standard errors of the means from groups of four mice.
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TABLE 2. Variant TCD8+ determinants across poxvirus species and strains
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E3140-148 is highly conserved, being present in all sequenced orthopoxviruses, with the determinant in nearly all cases being identical to that in VACV-WR. The exception is ECTV, in which the penultimate residue of the peptide is changed from Thr to Ile. This variant (VGPSNSPIF) is ranked as the highest H-2Dd-binding peptide in the ECTV homologue of E3 by Bimas and is predicted to be immunogenic.
Finally, the A52R ORF is absent in MVA and several other orthopoxviruses, but where present, the A5275-83 determinant is identical to that found in VACV-WR.
Observed conservation of TCD8+ determinants across orthopoxvirus species. The difficulties associated with working with VARV means that much smallpox vaccine development will go forward on the basis of conservation of determinant sequences among poxviruses and predictions of antigenicity. The use of poxviruses that infect mice and mapping of determinants allow us to test predictions of antigenic cross-reactivity across orthopoxvirus species. To this end, we determined TCD8+ responses of mice infected with VACV-WR, VACV-MVA, CPXV, or ECTV to peptides corresponding to all variants of the three VACV-WR determinants (Fig. 3). In each case, all variants were recognized by splenic TCD8+ from infected mice, but the largest response was always to the peptide encoded by the infecting virus (e.g., SPGAAGYDL for MVA- or CPXV-infected mice). This result was not surprising for SPGAAGYDL and VGPSNSPIF, both predicted to bind well to their MHC restriction element. For SNHAAGYDL, which is not predicted to bind H-2Ld, we were surprised to find that not only did TCD8+ from VACV-infected (WR and MVA) and CPXV-infected mice respond to this variant of F226-34, but ECTV was able to prime responses to this peptide in vivo.
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FIG. 3. Cross-reactivity between TCD8+ elicited by VACV-WR and variant peptides from other orthopoxviruses. In all panels, VACV-WR peptides are indicated by protein name; variants are F2(G) (SPGAAGYDL), F2(NH) (SNHAAGYDL), and E3(I) (VGPSNSPIF). (A) Mice were infected with the orthopoxvirus shown in the top left of each graph: VACV-WR and MVA, 106 and 108 PFU, respectively, i.p.; CPXV, 105 PFU i.p.; and ECTV-TK, 2 x 107 PFU s.c. in the rear leg shank. Splenic TCD8+ responses to peptides were measured by ICS after 7 days (VACV strains) and 8 days (CPXV and ECTV). Data are percentages of TCD8+ that produce IFN- in ex vivo stimulations with peptides. Means and standard errors of the means for groups of four or five mice are plotted and are representative of repeated experiments. (B and C) A TCD8+ line was derived from VACV-WR immune splenocytes by five restimulations with SPYAAGYDL in vitro and tested for cross-reactivity with variant peptides at various concentrations by ICS (B) and to peptides and virus-infected cells by cytotoxicity assay (C). (B, left) Percent TCD8+ that produce IFN- after a short stimulation with the peptide shown (circle, SPYAAGYDL; square, SPGAAGYDL; triangle, SNHAAGYDL); (B, right) the same data presented as percentages of the maximum response. Panel C shows percent specific lysis at the E:T ratios indicated for this TCD8+ line against ECTV-infected (ECTV, unfilled triangle) or VACV-WR-infected (VACV, unfilled circle) P815 cells or peptide-pulsed P815 as indicated above the graph (symbols as in panel B).
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We then returned to the issue of cross-reactivity between variant peptides, and to investigate this further, we measured the actual affinities of all peptide variants for their restricting MHC (Table 2) and generated a TCD8+-reactive line to F226-34 (SPYAAGYDL) and estimated the size and avidity of cross-reactive TCD8+ populations using peptide titrations in ICS (Fig. 3B). The affinity measurements showed that despite a prediction to the contrary in the case of SNHAAGYDL, all peptides bound their restriction element with very high (<20 nM) affinity. In the TCD8+ line experiments, nearly 85% of the cells in the F226-34 line responded to SPYAAGYDL at 1 µM, but only half of these cells were cross-reactive with SPGAAGYDL and around a quarter with SNHAAGYDL. These data were also plotted as percentages of maximum stimulation (left graph in Fig. 3B) to give a better comparison of the relative sensitivities of the TCD8+ populations that cross-reacted to the peptides. Comparison of these two plots indicates that while roughly twice as many SPYAAGYDL cells in the culture recognized SPGAAGYDL compared with recognition of SNHAAGYDL, the overall sensitivity of the cross-reactive TCD8+ for each case was similar. Given that these peptides have similar affinities for H-2Ld (Table 2), these data suggest that the cross-reactive T-cell populations recognizing these variants have similar avidity. Finally, to demonstrate that the cross-reactivity between SPYAAGYDL and SNHAAGYDL can lead to antiviral killing, we tested the ability of the same TCD8+ line to lyse VACV- or ECTV-infected cells (Fig. 3c). TCD8+ specific for F226-34 from VACV were able to lyse cells pulsed with both forms of F226-34 as well as those infected with VACV and with ECTV. These data, combined with those from work with H-2b-restricted peptides (26), show that current bioinformatic methods are not always able to predict cross-reactivities of TCD8+ responses across orthopoxvirus species and highlight the need for refined predictive algorithms supported by more experimental data.
Concluding remarks.
We have mapped the first TCD8+ determinants for VACV in BALB/c (and other H-2d haplotype) mice, and these three determinants were responsible for a significant proportion of the total TCD8+ response to VACV. Synthetic peptides based on each determinant were recognized at physiologically relevant concentrations in in vitro assays, and approximately 70% of the TCD8+ that responded to each made TNF as well as IFN-
. Finally, a comparison of predicted and actual cross-reactivities of these determinants across four different orthopoxviruses revealed an unexpectedly cross-reactive variant peptide encoded by ECTV.
This work was funded by the NIAID-NIH intramural program and grants from the NHMRC (Australia) to D.C.T. (Howard Florey Centenary Fellowship no. 224273) and G.K. (no. 153836), the Howard Hughes Medical Institute (G.K.), and NIAID-NIH to A.S. and J.S. (R01 grant AI56268 and contract N01-AI-40023). I.G.S. is the recipient of an ANU Ph.D. scholarship.
Present address: Coridon, Level 2 Research Extension Building 1, Princess Alexandra Hospital, Ipswich Rd., Buranda QLD 4102, Australia. ![]()
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