Cross-presentation and genome-wide screening reveal candidate T cells antigens for a herpes simplex virus type 1 vaccine

Herpes simplex virus type 1 (HSV-1) not only causes painful recurrent oral-labial infections, it can also cause permanent brain damage and blindness. There is currently no HSV-1 vaccine. An effective vaccine must stimulate coordinated T cell responses, but the large size of the genome and the low frequency of HSV-1–specific T cells have hampered the search for the most effective T cell antigens for inclusion in a candidate vaccine. We have now developed what we believe to be novel methods to efficiently generate a genome-wide map of the responsiveness of HSV-1–specific T cells, and demonstrate the applicability of these methods to a second complex microbe, vaccinia virus. We used cross-presentation and CD137 activation–based FACS to enrich for polyclonal CD8⁺ T effector T cells. The HSV-1 proteome was prepared in a flexible format for analyzing both CD8⁺ and CD4⁺ T cells from study participants. Scans with participant-specific panels of artificial APCs identified an oligospecific response in each individual. Parallel CD137-based CD4⁺ T cell research showed discrete oligospecific recognition of HSV-1 antigens. Unexpectedly, the two HSV-1 proteins not previously considered as vaccine candidates elicited both CD8⁺ and CD4⁺ T cell responses in most HSV-1–infected individuals. In this era of microbial genomics, our methods — also demonstrated in principle for vaccinia virus for both CD8⁺ and CD4⁺ T cells — should be broadly applicable to the selection of T cell antigens for inclusion in candidate vaccines for many pathogens.

Herpes simplex virus type 1 (HSV-1) infects 60% of the US population and has a significant cumulative health care burden in addition to causing painful recurrent oral-labial infections. For example, brain and eye infections can cause permanent damage or blindness (1). HSV-1 also causes approximately 50% of clinical first-episode genital herpes in the United States. Vaccines for HSV that have been tested thus far have failed in clinical trials, including a recent phase III trial of an adjuvanted glycoprotein D (gD2) product (2). This vaccine elicits antibody and CD4⁺ T cell responses but fails to induce CD8 responses. Newer platforms can elicit CD8⁺ and CD4⁺ cells, but they require rationally selected T cell antigens. We therefore developed methods to permit measurement of both CD8 and CD4 responses to the complete HSV-1 proteome to begin rational prioritization of next-generation vaccine candidates.

Several recent observations support the concept that an effective HSV vaccine will need to induce coordinated CD8⁺ and CD4⁺ T cell responses. HSV-1–specific CD8⁺ T cells localize to the site of HSV-1 infection in human and murine trigeminal ganglia (TG) (3–5), and both HSV-specific CD8⁺ and CD4⁺ T cells localize to acute and healed sites of skin infection in mice and humans, suggesting that optimally programmed memory cells could monitor for infection or reactivation (6–8). In animals, HSV ganglionic load correlates with reactivation frequency, so pre-equipping an individual with HSV-specific CD8⁺ T cells could reduce seeding of the ganglia, even if a primary infection occurs in recipients of a non-sterilizing vaccine, and ameliorate the chronic disease (9, 10). Strong CD8⁺ responses can be protective in HSV infection–specific mouse models (11). In murine protection models based on attenuated live virus or DNA vaccines, protection is more typically CD4 dependent, and in humans, HSV disease worsens with CD4 depletion in untreated human immunodeficiency virus type 1 (HIV-1) infection (12, 13).

The breadth and specificity of HSV-1–specific T cells in humans is largely unknown. The virus has a large, 152-kb genome encoding about 77 polypeptides (14, 15). BenMohamed et al. demonstrated A*0201-restricted responses to HSV-1 glycoprotein D (16, 17). A limited number of CD8 epitopes discovered in the context of HSV-2 research are sequence identical and thus cross-reactive with HSV-1. In HSV-1–infected human eyes, we have demonstrated CD4 reactivity with proteins in the viral tegument encoded by genes UL21, UL46, UL47, and UL49 (18–23). Envelope glycoproteins gD1 and gB1 are also known CD4 antigens (24).

The rules governing CD8 specificity are an important issue for HSV vaccine design. HSV genes are expressed in sequential, coordinated kinetic waves during the viral replication cycle, and a subset of proteins are present in virions and injected into cells upon viral entry. Some replication-incompetent whole HSV vaccines are blocked at the DNA replication step, such that true late proteins, which are only made after DNA replication, are not expressed (25). Other strains have a later replication block, with true late proteins being synthesized in the cytoplasm of infected cells (26). This property is shared by attenuated but replication-competent candidates (27). One of our goals was therefore to determine whether the CD8 response is weighted toward any specific kinetic or structural subset of HSV-1 proteins.

HSV immune evasion and the low abundance of HSV-specific CD8⁺ cells in human blood have made the study of HSV-specific T cell responses difficult. Inhibition of transporter associated with antigen presentation (TAP), downregulation of HLA class I (28, 29), decreased DC co-stimulation (30), and disruption of TCR signaling (31, 32) mediated by various HSV genes all likely contribute to difficulties with direct presentation in in vitro settings. In contrast, murine HSV data show that both the priming of naive CD8 responses and the recall of memory CD8⁺ cells use cross- rather than direct priming and presentation (33–38). We have previously shown that human monocyte-derived DCs (moDCs) can cross-present HSV-2 to memory HSV-2–specific CD8s (39). In this report, we harnessed cross-presentation to stimulate HSV-1–specific CD8⁺ T cells, while CD4⁺ memory cells were reactivated with whole killed antigen. CD137 was then used to radically enrich HSV-1–specific T cells. CD137 is a tumor necrosis factor receptor family protein that identifies recently activated CD4⁺ and CD8⁺ T cells (40–42). A near complete collection of HSV-1 molecular clones was deployed in specific CD8 and CD4 formats to perform genome-wide scans of these polyclonal virus-specific T cells. Our data identified the proteins expressed by HSV-1 genes UL39 and UL46, previously not known to be CD8⁺ T cell antigens, as rational vaccine candidates for the elicitation of coordinated CD8 and CD4 responses. In contrast, gD1, the homolog of gD2, was a poor CD8 antigen.

To test the broad applicability of our methods, we evaluated vaccinia virus, a microbe with more than 200 genes. We studied whether moDC cross-presentation and CD137-based methods using whole virus would enrich vaccinia-reactive CD8⁺ and CD4⁺ T cells. The affirmative results suggest that a modular approach to T cell antigen discovery and prioritization, modified on a case-by-case basis to reflect the biology of specific microbes, should be laterally transferable to challenging pathogens with large genomes.

HSV-1–specific CD8⁺ T cells can be detected and enriched by cross-presentation. We studied 7 HSV-1–seropositive individuals (Table 1), in whom we measured HSV-1–specific T cell responses in fine detail. In each case, exposure of CD8⁺ cells from PBMCs to autologous, HSV-1 antigen–loaded moDCs for 20 hours resulted in detectable CD137 responses among live CD3⁺CD8⁺ cells (representative participant, Figure 1A). We observed that specific expression of CD137 was usually somewhat higher than for IFN-γ (Table 2). Among 3 individuals seronegative for HSV-1 and HSV-2 (individuals 12–14, Table 1), two had very low CD137 and cytokine CD8 responses, while participant 13 had detectable responses in both assays (Table 2).

Figure 1

Use of CD137 to detect and enrich HSV-1–specific CD8⁺ T cells from blood. (A) Gated live, CD3⁺ lymphocyte forward/side scatter window cells analyzed for CD8 and CD137 after admixture of selected CD8⁺ cells with autologous moDCs loaded with mock- or HSV-1–infected HeLa cell debris (see Methods). Numbers are percentages of cells in indicated quadrants. Data for HSV-1–infected participant 1 and HSV-uninfected participant 12 are shown. Small boxes indicate approximate gates for FACS. (B) Reactivity of participant 1 polyclonal expanded responder cell line derived from CD3⁺CD8⁺ CD137^hi or CD137^lo cells after exposure to mock- or HSV-1–infected autologous B-LCLs or control stimuli for 18 hours. Responder cells were initially gated using dump-gating of CFSE-labeled APCs (data not shown) and for CD3 and CD8 (left), and analyzed for intracellular IFN-γ. Numbers are percentages of cells in indicated quadrants. iono, ionomycin.

Table 1

Participants studied in this report

Table 2

Direct ex vivo expression of intracellular IFN-γ or surface CD137 by live, CD3⁺CD8⁺ cells after cross-presentation by autologous moDCs loaded with HSV-1 or control antigen

An advantage of using CD137 to detect HSV-1–reactive CD8⁺ cells is the ability to sort and expand these cells for downstream testing. Sorted, polyclonal CD3⁺CD8⁺CD137^hi cells and control CD3⁺CD8⁺CD137^lo cells were expanded with a nonspecific mitogen. Resultant bulk populations were tested using autologous APCs infected by HSV-1. Significant proportions of the sorted, expanded CD137^hi cells selectively recognized the infected APCs (representative data for participant 1 after 2 cell expansions in Figure 1B; all individuals in Table 3), while the CD137^lo cells were nonreactive. Cytotoxicity was used to assess the antiviral effector function of the sorted, expanded cells. Brisk, self-restricted killing was noted for most participants (Table 3).

Table 3

Recognition of HSV-1 by polyclonal, twice mitogen-expanded CD3⁺CD8⁺ PBMCs selected on the basis of CD137 expression after cross-presentation of HSV-1 by moDCs

Detection and HLA restriction of HSV-1 antigen–specific CD8⁺ T cells. We cryopreserved more than 10⁸ responder cells/individual and interrogated their responses with panels of artificial APCs (aAPCs), expressing one of the participant’s HLA-A, -B, or -C molecules, and specific fragments of HSV-1 genetic material. Full-length genes or fragments, together covering a total of 74 HSV-1 ORFs, were cloned into a custom vector suitable for expression in aAPCs. Transfection efficiency for HLA class I was typically 5%–20% at 48 hours (data not shown). Transfection efficiencies for the HSV-1 constructs were typically at least 10% (Supplemental Figure 1; supplemental material available online with this article; doi: 10.1172/JCI60556DS1) as monitored with EGFP.

We completed CD8 ORFeome scans for every HLA-A, -B, and -C in 7 HSV-1–infected individuals (Table 1). T cell activation was monitored by IFN-γ secretion after addition of polyclonal CD8 responders to the co-transfected aAPCs. Due to near-homozygosity in one participant per locus, some participants had one scan at HLA-A, -B, or -C. We used 21 distinct HLA class I cDNA molecules in all. The most frequently studied alleles were A*0201 (4 individuals) and A*0101, B*4402, and Cw0701 (3 individuals each).

We observed discrete IFN-γ responses with very low backgrounds. A representative set of genome-wide screens for participant 1 (Figures 2, 3, and4) showed that each HLA allele had discrete CD8 reactivities. For example, genes UL39 and UL48 had strong reactivity restricted by HLA-A*0101, confirmed with synthetic peptides including two distinct epitopes in the UL48-endoded protein (Figure 5). Overall, there were 122 reactive combinations of HLA class I molecules and HSV-1 ORFs (Figure 6). The number of CD8 ORF-level hits per person ranged from 10 to 27, with a median of 17 and mean ± SD of 17 ± 7. Among these CD8 ORF-level hits, HLA-A was the most frequently used locus and HLA-C the least, with a mean ± SD of 10 ± 4.0, 6.6 ± 4.0, and 1.3 ± 1.7 CD8 ORF-level hits at the A, B, and C loci, respectively. All 6 HLA-A alleles and 6 of 7 HLA-B alleles had one or more responses, while 3 of the 8 HLA-C alleles (0102, 0402, and 0704) did not. Overall, 28 of the 39 (72%) genome-wide screens yielded one or more reactive HSV-1 ORFs, with a range from 0 to a maximum of 13 for HLA-A*3503 in participant 6, and a mean ± SD of 5.2 ± 2.3, 3.5 ± 3.8, and 0.6 ± 1.0 CD8 ORF-level hits in individual HLA-A, -B, and -C allele screens, respectively.

Figure 2

Representative data from participant 1 (Table 1) for CD8⁺ T cell reactivity with HSV-1 ORFs and peptides. IFN-γ secretion by polyclonal expanded responder cell line derived from CD3⁺CD137^hi cells exposed to aAPCs expressing the indicated HLA-A molecules and the HSV-1 ORFs arrayed in nominal genomic order on the x axis. The names of HSV-1 ORFs driving two representative positive responses are indicated for HLA-A*0101.

Figure 3

Representative data from participant 1 (Figure 2 and Table 1) for CD8⁺ T cell reactivity with HSV-1 ORFs and peptides. IFN-γ secretion by polyclonal expanded responder cell line derived from CD3⁺CD137^hi cells exposed to aAPCs expressing the indicated HLA-B molecules and the HSV-1 ORFs arrayed in nominal genomic order on the x axis.

Figure 4

Representative data from participant 1 (Figures 2 and 3 and Table 1) for CD8⁺ T cell reactivity with HSV-1 ORFs and peptides. IFN-γ secretion by polyclonal expanded responder cell line derived from CD3⁺CD137^hi cells exposed to aAPCs expressing the indicated HLA-C molecules and the HSV-1 ORFs arrayed in nominal genomic order on the x axis.

Figure 5

Representative analyses of polyclonal HSV-1–reactive CD8⁺ cells from the same individual represented in Figures 2–4 probed for reactivity with individual HSV-1 peptides derived from the ORFs indicated below the plots, or negative or positive controls (Mock and SEB). Numbers are percentages of cells in the upper-right quadrants.

Figure 6

HLA allele– and HSV-1 ORF-level IFN-γ immune signature of CD8⁺ cells in PBMCs of 7 individuals infected with HSV-1. Participant identities are listed below the figure. Each column represents an individual HLA-ORFeome screen. The HLA-A, -B, or -C alleles used are indicated at the top. Each row represents the integrated data for an HSV-1 ORF, with ORFs listed in nominal genomic order from RL1 (encoding γ34.5 protein) at top to RS1 (encoding protein ICP4) at bottom, with gene names from GenBank NC_001806.1. A red cell shows that specific IFN-γ secretion was detected for the intersecting HLA allele and HSV-1 ORF. Data for ORFs expressed as more than one fragment or exon are simplified to a yes/no call. UL36 amino acid coverage was partial (see Discussion). Black arrows indicate, from top to bottom, genes UL39, UL46, and US6.

HSV-1 ORFs eliciting CD8 responses enriched by cross-presentation. Overall, 40 distinct HSV-1 polypeptides were found to elicit CD8⁺ IFN-γ responses among the 7 participants. This represents 54% of the 74 unique proteins studied (Figure 6). These proteins had diverse expression kinetics, structural, and functional roles, as briefly annotated (Supplemental Table 2) and detailed in the primary literature (reviewed in ref. 1). Each immediate early protein expressed with α kinetics was represented, except for ICP47, a short polypeptide, as were early, leaky late, and true late polypeptides. Nonstructural proteins and structural proteins in the capsid, tegument, and envelope were all targeted by CD8⁺ T cells. The most population-prevalent CD8 antigen was encoded by UL39. This 1,137-amino-acid-long polypeptide is the large subunit of ribonucleotide reductase, is not detected in virions, and is a virulence factor in vivo but dispensable in vitro. UL39 was recognized in 11 of the 39 screens, in 6 of the 7 individuals, and was restricted by 7 distinct HLA alleles: A*0101, A*0201, A*2402, A*6801, B*3503, B*5801, and Cw0202. The next most prevalently recognized protein was encoded by the abundant virion structural protein VP11/12, which is encoded by UL46. This protein is nonessential in vitro (1). UL46 was recognized in 10 screens and 5 participants and also restricted by 7 distinct alleles: A*0101, A*0201, A*2402, A*2601, A*2902, B*4402, and B*5101.

CD8 responses to HSV-1 proteins gD1 and gB1 were of special interest because they share high sequence homology with HSV-2 proteins that have been used as vaccine candidates (2, 43–45). HLA-A*0201–restricted CD8 epitopes have been previously reported in both HSV-1 and HSV-2 (16, 17). Both proteins were well expressed in the pEXP103 system (Supplemental Figure 2, A and B). Two of 39 HLA-level screens showed reactivity with gD1 (Figure 6), for either HLA-B*1516 or HLA-B*3503. Among the 4 individuals with HLA-A*0201 or a close variant, none had A*0201-restricted responses to gD1. We additionally tested polyclonal HSV-reactive CD8⁺ T cell lines from these individuals with three previously reported (16) A*0201-restricted synthetic peptides in gD that are sequence-identical in HSV-1 and HSV-2. Responses were not detected (Supplemental Figure 2C). In contrast, we demonstrated CD8 recognition of gB1 by 6 distinct HLA alleles and in 4 of 7 individuals.

Definition of HSV-1 peptide epitopes recognized by CD8⁺ T cells enriched by cross-presentation. To test for the presence of discrete peptide epitopes, we selected a subset of the CD8 antigens (Figure 6) that used HLA alleles with high population prevalence and had well-developed peptide binding prediction algorithms. We tested peptides from 24 distinct HSV-1 ORFs for potential HLA-A*0101–, -A*0201–, -A*2402–, -A*2902–, or -B*0702–restricted peptide epitopes. Bulk CD137^hi-selected CD8⁺ cells were tested for IFN-γ expression by intracellular cytokine cytometry (ICC) using autologous PBMCs as APCs. DMSO negative control gave very low background, such that tight groupings of IFN-γ⁺ CD8⁺ T cells could be discerned for antigenic peptides (representative data, Figure 5; full data, Supplemental Figure 3). Overlapping reactive 9- and 10-mer peptides were tallied as a single novel epitope. Overall, we defined 45 distinct HSV-1 CD8 epitopes (Table 4) in 22 ORFs. Several reactive ORFs had more than one constituent CD8 peptide epitope (Table 4).

Table 4

HSV-1 CD8 epitopes and HSV-2 homologs

CD8 responses in direct PBMC assays. The CD8⁺ T cell line data above are qualitative rather than quantitative. The enrichment afforded by cross-presentation and cell selection could detect responses that were below the limit of detection in direct PBMC samples, and there is also the possibility we were detecting in vitro priming by moDCs. Epitope-specific responses in direct PBMC assays cannot represent in vitro priming and are amenable to detailed phenotypic studies using tetramers and ICC. We therefore used IFN-γ ELISPOT to survey and rank epitope-specific responses for further studies. PBMCs from 20 HLA-appropriate individuals with HSV-1 infection were matched with CD8 peptide epitopes with known HLA restriction. We tested 40 of the 45 CD8 epitopes (Table 4) as detailed in Methods. The participants included the discovery cohort (Table 1) and 13 additional HSV-1–infected individuals. Each individual had a strong IFN-γ response to whole UV HSV-1 antigen (likely CD4⁺ cells) and no spot-forming units (SFU) for DMSO negative control (data not shown).

Among 256 HLA-matched combinations of PBMCs and HSV-1 peptides in the overall set, 23 (9.0%) were positive (red cells with integers in Figure 7). Twelve of 20 (60%) individuals had from 1 to 5 peptide-specific responses in direct PBMC testing. Among the 40 CD8 peptide epitopes tested, 12 (30%) were positive in 1 or more HLA-matched individuals. The number of net IFN-γ ELISPOT⁺ cells ranged from 11 to 136 SFU/10⁶ PBMCs. The highest rate of positivity was for the HLA-A*0201 peptides, with 6 of 9 epitopes positive in at least 1 individual, and 2 individuals positive for 4 distinct A*0201 peptides. The “hits” in the HLA-ORF screens that were confirmed by direct PBMC testing were biologically present above the threshold of the direct ELISPOT test. Some individuals with positive ORF-level responses in HLA-specific screens (red in Figure 6) did not react with the peptides tested (blue in Figure 7). Peptide-reactive cells could be present below the limit of detection ex vivo. Alternatively, one or more undiscovered HLA-restricted epitopes accounted for the ORF-level positive responses (Figure 6).

Figure 7

Graphical summary of direct PBMC IFN-γ ELISPOT. HSV-1 peptides from Table 4 (n = 40, detailed in Methods) were tested with PBMCs from 20 individuals with HSV-1 infection. Each column represents one participant; 1–7 are detailed in Table 1. Each row lists a peptide with 1 or more positive ELISPOT results. Green cells represent possible reactivities based on the participant bearing an HLA allele corresponding to the peptide tested, but for which the ORFeome screen with the listed HLA allele and ORF, and peptide ELISPOT, were negative. Blue cells are similar, but the ORFeome screen was positive and the peptide ELISPOT with the indicated peptide was negative. Red cells represent ORFs for which both the ORFeome screen with the listed HLA allele and ORF, and the ELISPOT for at least one peptide in the ORF, were positive. Numbers in red cells are positive ELISPOT results in units of net IFN-γ SFU/10⁶ PBMCs.

HSV-1 ORFs stimulating population-prevalent CD4 responses. As noted above, measurement of unmanipulated PBMCs is limited by the low frequency of HSV-1–reactive CD4⁺ cells and the need for highly purified recombinant proteins or a very large peptide set. We therefore enriched and expanded HSV-1–reactive CD4⁺ T cells using protocols designed to yield large numbers of polyclonal responder cells. The initial stimulation used whole, cell-associated, UV-killed HSV-1, a format previously shown to restimulate CD4⁺ T cells specific for a variety of structural and nonstructural proteins in the context of HSV-2 (46). After 20 hours, a small percentage of live CD3⁺CD4⁺ cells in PBMCs specifically expressed CD137 (representative participant, Figure 8A). Cell lines created by sort purification and expansion with nonspecific mitogens were highly enriched for HSV-1–reactive CD4⁺ cells, while sorted CD137^lo cells were nonreactive (Figure 8A shows data after 2 cell expansions; enrichment was similar after the first expansion, data not shown).

Figure 8

Use of CD137 expression to enrich HSV-1–specific CD4⁺ T cells, and representative raw data from HSV-1 proteome-wide scan. (A) Top 2 panels show expression of CD137 by PBMCs after 20 hours of exposure to whole cell–associated UV-killed mock or HSV-1 lysate. Dot plots were gated for live, CD3⁺ cells in the lymphocyte forward/side scatter region. Numbers are percentages of cells in the upper-right quadrant. Small boxes indicate approximate gates for FACS. Bottom 6 panels show reactivity of polyclonal twice-expanded responder cell lines derived from CD3⁺CD4⁺CD137^hi or CD3⁺CD4⁺CD137^lo cells, after 18 hours reexposure to autologous APCs and whole cell–associated UV-killed mock or HSV-1 lysate. APCs were CFSE dump-gated and responder cells stained intracellularly for IFN-γ and IL-2. Numbers are percentages of cells in indicated quadrants. (B) Representative screen of polyclonal HSV-1–reactive CD4⁺ cells to each HSV-1 protein or fragment, whole HSV-1–positive control, and irrelevant microbial negative control proteins. Data are mean of duplicate assays. Red line is cutoff for positive responses calculated as described in Methods.

We expressed proteins covering the large majority of the HSV-1 proteome (Supplemental Table 1) using an in vitro bacterial expression system. Anti–6-His IB showed specific staining (data not shown). We titered the ORFeome set in preliminary proliferation assays and found that a dilution of 1:5,000 it gave optimal responses with low background (data not shown). We further checked potency and identity with a CD4⁺ T cell clone specific for HSV-1 protein VP22 (gene UL49) (18) and noted strong, specific responses (Supplemental Figure 4).

Polyclonal CD137^hi CD4⁺ cell lines showed discrete patterns of reactivity when assayed against the protein set (representative participant, Figure 8B) in each of 11 individuals, including those with detailed CD8 studies (Table 1). The average number of HSV-1 ORFs recognized per individual was 22.8 ± 7.0 (mean ± SD). Overall, 52 of the 74 (70%) unique HSV-1 polypeptides were recognized at least once. On a population basis, the most prevalent CD4 responses were noted for envelope glycoproteins gB1 and gD1, and tegument protein VP11/12, encoded by gene UL46, discussed above for CD8⁺ cells. Each was recognized by 11 of 11 individuals (100%). Inspection of the overlap between CD8 and CD4 antigens (Figure 9) showed that the proteins encoded by UL39 and UL46 were frequently recognized. Grouping of HSV-1 proteins by their kinetics of expression during viral replication (1) indicates that true late proteins are less commonly recognized by CD8⁺ cells than are proteins in other classes.

Figure 9

Graphical representation of CD4 and CD8 reactivity to HSV-1 ORFs in PBMCs from 7 HSV-1–infected individuals, indicated in the rows. Each column is an HSV-1 ORF. The ORFs are grouped by their kinetic expression during viral replication. White indicates no reactivity.

Application to vaccinia virus. Participant 9 from a previous report (47) was re-vaccinated with vaccinia 20 months prior to phlebotomy. Using cross-presentation for CD8⁺ T cells, followed by CD137 detection outlined exactly as done for HSV-1, we detected low but specific CD8 reactivity at 20 hours. Selected, expanded CD137^hi but not CD137^lo cells were highly enriched in vaccinia virus–specific CD8⁺ T cells (Figure 10A), and these cells had specific cytotoxicity (Figure 10B). Participant 8 (47), who had been re-vaccinated 40 months prior to study, was studied for CD4 responses. We used UV-inactivated whole vaccinia virus and CD137-based selection, again as detailed for HSV-1. The CD137^hi-origin bulk cells were very highly enriched for T cells making IFN-γ with or without IL-2 in response to vaccinia, while these were essentially absent from CD137^lo cells (Figure 10C). All cell populations responded to the positive control PMA/ionomycin stimulation, albeit with varying cytokine patterns. Similar results were obtained for several vaccinia-immune individuals. The CD8⁺ and CD4⁺ T cell enrichment methods (outlined in Figure 11) are thus applicable to two large-genome microbes. Downstream CD4 analyses showed responses to discrete vaccinia ORFs (unpublished observations).

Figure 10

Detection and enrichment of vaccinia-specific CD8⁺ and CD4⁺ T cells. (A) Left panels show expression of CD137 after 20 hours of exposure of CD8⁺ T cells to cross-presented mock or vaccinia antigen. Small boxes indicate approximate gates for FACS. Numbers are percent of total gated live CD3⁺ lymphocytes in each quadrant. Right panels show IFN-γ expression by bulk, expanded CD8⁺ CD137^hi or CD137^lo cells in response to exposure to autologous B-LCLs in the absence or presence of vaccinia infection, or positive control stimulus. Numbers are percentages of gated live, CD3⁺ lymphocytes in each quadrant. (B) Cytolytic activity of bulk, expanded CD8⁺CD137^hi cells to autologous or allogeneic APCs with or without vaccinia infection. (C) Left panels show expression of CD137 by CD4⁺ T cells after 20 hours of exposure of PBMCs to UV-inactivated, cell-associated mock or vaccinia antigen. Small boxes indicate approximate gates for FACS. Numbers are percentages of gated live, CD3⁺ lymphocytes in each quadrant. Right panels show IFN-γ and IL-2 expression of polyclonal expanded CD4⁺ CD137^hi or CD137^lo cells to autologous APCs and mock or vaccinia antigen. APCs were CFSE dump-gated. Numbers are percentages of live, CD4⁺ cells in each quadrant.

Figure 11

Schematic overview of the high-throughput T cell antigen discovery pathway. See text for details. In this report, the microbe (left) was a virus, HSV-1, but the workflow can also be adapted to bacteria or parasites. A microbial ORF library is initially cloned in a flexible format and subcloned (not shown) into both a custom protein expression vector for CD4 assays and a custom transient expression vector for CD8 assays. The CD4 workflow (top) stimulates PBMCs with whole killed microbe and detects and isolates microbe-specific CD4⁺ T cells based on differential CD137 expression followed by expansion. The polyclonal CD4⁺ responder cells are then assayed against the protein library made in vitro from the secondary protein expression clone set. The CD8 workflow (bottom) uses cross-presentation by microbial antigen-laden DCs to stimulate CD8⁺ T cells from PBMCs. After CD137-based selection and expansion, effector cells are assayed for reactivity with panels of person-specific aAPCs made by co-transfection of Cos7 cells with participant HLA class I cDNA and the transient transfection microbial ORF set. The integrated assays assign each ORF a yes/no result for each participant for CD4⁺ and CD8⁺ T cells (turquoise).

HSV-1 is an important human pathogen, but there are no vaccines in active clinical development. In this report, we have shown that the proteins encoded by HSV-1 genes UL39 and UL46 have coordinated CD8 and CD4 immunogenicity in most individuals and are therefore rational vaccine candidates. We have provided an estimate of the complexity of the response, documented clustering of responses based on HLA type, and defined more than 40 novel CD8 T cell epitopes. We have identified a new hierarchy of responses based on HLA locus, with HLA-A more frequently responsible for antigen presentation than HLA-B, and HLA C having a minor contribution. Parallel studies determined that infected humans recognize a mean of 17 and 23 HSV-1 ORFs as CD8 and CD4 antigens, respectively. With the exceptions noted in the Introduction and Results, to our knowledge, the vast majority of the antigenic reactivities and epitopes we have defined are novel. We also showed applicability to another large-genome virus and anticipate that these systems may be useful for many pathogens.

T cell responses to pathogens have been difficult to access for several reasons. Microbe-specific T cells can occur at low abundance in the blood, such that an unbiased pre-enrichment step is helpful for new antigen or epitope discovery. Sylwester et al.’s probe of the response to the CMV proteome using peptides and direct PBMC ICC was enabled by the high overall abundance of T cell responses to CMV (48). Responses to EBV are also large, such that a direct PBMC approach to CD8 responses using a cloned partial ORFeome has yielded hits (49). Indeed, the low magnitude of direct PBMC IFN-γ ELISPOT responses to single HSV-1 peptides in the current report contrast with the high-magnitude responses to single epitopes noted in CMV and EBV (48, 50).

We have shown that restimulation methods tailored for CD8⁺ or CD4⁺ T cells, based on the biology of antigen presentation, can be used without change for two distinct viruses. Once responder cells are enriched and expanded, the large microbial genomes still harbor myriad potential epitopes that are challenging to decode. In this report, we first assigned CD8 reactivity at the level of HSV-1 ORFs, using efficient plasmid sets. Limited use of peptide binding algorithms and peptide synthesis efficiently confirmed antigenicity to the epitope level. The new, validated peptide reagents were in turn positive in a proportion of additional HLA-appropriate subjects in direct ex vivo assays. Even in our limited study population, CD8⁺ T cells from different individuals frequently had reactivity, in our primary co-transfection screens, with the same HSV-1 ORFs when studied using shared HLA cDNA molecules. For example, each HLA-A*0101–bearing donor had CD8⁺ T cells recognizing the HSV-1 ORFs UL1 and UL48 (Figure 6). Clustering studies to measure this tendency will be the subject of future analyses.

In addition to identifying UL39 and UL46 as rational candidate subunit vaccines, our data have implications for the design of whole virus formats. In fact, the diversity of the CD8 response, with an average of 17 antigens per person, implies that a whole virus rather than a subunit approach to vaccination for HSV-1 is most likely to mimic the immune response to natural infection. Globally, we found that broad kinetic and structural and functional spectra of HSV-1 proteins were recognized by the human CD8 response. Therefore, either replication-incompetent or attenuated replication-competent vaccine formats have the potential to stimulate broad CD8 responses in most individuals. Among whole HSV vaccine candidates that replicate discontinuously in normal cells, those that allow expression to proceed relatively completely may be quite rational (25, 26). To explore the virological rules of HSV-1 T cell antigenicity, we scored each protein dichotomously for CD8 responses in the study population, and then categorized each protein studied as immediate early, early, late but not otherwise characterized, early late with synthesis prior to DNA replication, or true late with expression only after DNA replication (1). We also recorded, for each HSV-1 protein, its absence, detection at less than 1%, or detection at greater than 1% of adjusted virion mass using mass spectroscopy data of purified virions (51). These analyses disclosed a weighting of CD8 responses toward HSV-1 proteins expressed prior to HSV-1 DNA replication, and toward abundant virion polypeptides. Specifically, only 3 of 17 true late proteins (18%) were recognized by CD8⁺ cells. In contrast, 4 of 5 immediate early proteins (80%), 9 of 12 early proteins (75%), 12 of 19 early late proteins (63%), 12 of 20 late proteins not specified as early or late (60%), and 0 of 1 proteins with no specified expression kinetics (0%) were CD8 antigens (highlighted in Supplemental Figure 5 using Figure 9 data and expression classifications from a standard text; ref. 1). Among the more abundant virion proteins, 17 of 23 (74%) were positive for CD8 responses. In contrast, only 23 of 51 (45%) proteins either absent from virions or present at levels less than 1% were CD8 antigens. The population prevalence for CD4 responses did not segregate by HSV-1 kinetics or structural class. Our data suggest that whole-virus HSV-1 format vaccines that express most proteins normally made prior to DNA synthesis, or that can be dosed to provide a large mass of virion input proteins, should retain the potential to stimulate broad CD8 responses.

A vaccine covering HSV-1 and HSV-2 would be desirable. Half of the minimal HSV-1 CD8 epitopes defined in this report are sequence-identical in HSV-1 and HSV-2 and appropriate for candidate type–common vaccines. Indeed, the HSV-2 homologs of three epitopes — HLA-A*0101/HSV-1 UL39 512–520, HLA-A*0201/HSV-1 UL25 367–375, and HLA-A*0201/HSV-1 UL27 448–456 — were found in our prior HSV-2 work (52–54). HSV CD8 epitopes can also tolerate amino acid substitutions, as exemplified by UL46 354–362 of HSV-1 and HSV-2, differing at amino acid 2, and by ICP0 HSV-1 698–706 and its homolog HSV-2 ICP0 742–750, differing at amino acids 1 and 3. It is certainly possible that cross-reactive T cells could be involved in cross-protection against some aspects of HSV-2 infection or severity observed in HSV-1–infected individuals (55). Most of our subjects were dually infected with both HSV types. Future cross-sectional studies comparing immune responses to HSV-1 in the presence or absence of HSV-2 coinfection could clarify the extent to which each infection contributes to the cross-reactive repertoire.

With regard to effector function, we showed that bulk HSV-specific CD8⁺ T cells enriched using cross-presentation and CD137 have brisk virus-specific cytotoxicity. We plan to enrich peptide-specific CD8⁺ cells with peptides (56) or tetramers (57) and study recognition of HSV-1–infected skin cells to more closely mimic physiologic target cells. The Cos-7 system has not been characterized for use in CTL assays, so we will move to a viral infection system. In HSV-2 studies, T cells recognizing diverse antigens were able to lyse HSV-infected skin cells, but the specific conditions, such as the dose and time of infection and the requirement for de novo viral protein synthesis or for IFN-γ pretreatment (56, 58), differed between epitopes. With the larger panel of HSV-1 epitopes, we hope to establish general rules for CD8 recognition of physiologically relevant cells that could inform vaccinology. Future cross-sectional study of populations with defined levels of HSV-1 severity and longitudinal research during the ontogeny of primary immune responses or during reactivations in the chronic phase may also contribute correlates of severity and reactivation that could further influence vaccine design.

Interestingly, UL39 was a strong HSV-1 CD8 antigen in both humans and the one mouse MHC haplotype studied, H-2^b. UL39 is a virulence factor involved in evading innate immunity and apoptosis (59), such that immune targeting of UL39 may be advantageous to the host. The CD8 repertoire in infected C57BL/6 mice had a breadth of 19 HSV-1 epitopes. These were concentrated in only three ORFs, gB1 (gene UL27), UL39, and ICP8 (gene UL29) (60). The mice did not recognize immediate early HSV-1 polypeptides, while responses to ICP0, ICP4, ICP22, and ICP47 were detected in humans. In addition to MHC class I peptide binding preferences, these differences may reflect species-specific effects of HSV-1 HLA class I immune evasion genes (61) and the fact that the human exposure to HSV-1 antigen is chronic and intermittent, while HSV-1 typically does not recur in mice. We conclude that study of adaptive immunity in the natural host is a necessary counterpoint to the powerful manipulative experiments that are possible in experiment models of HSV-1 infection.

Several factors may have influenced our results. Our CD8 workflow used cross-presentation at the re-stimulation step, but then switched to direct present by aAPCs or peptide-loaded cells at the readout step. We observed that cross-presentation is efficient in presenting diverse HSV-1 proteins to CD8⁺ T cells. The HSV proteins ICP47 (gene US12) and vhs (gene UL41) inhibit direct presentation (30). We have previously re-stimulated memory CD8⁺ cells using direct presentation by HSV-infected B lymphoblastoid cell lines (B-LCLs), but this yielded a paucity of HSV-reactive CD8 clones reactive only with membrane glycoproteins (62). HSV-infected fibroblasts failed in this endeavor. Direct presentation by infected DCs might uncover epitopes specific for this pathway, although HSV infection harms various DCs and renders them defective for antigen presentation (63–65). Future studies will compare direct and cross-presentation at the re-stimulation stage.

Expression of the HSV-1 proteome was not totally complete. Genes UL15.5, UL20.5, UL27.5, and UL43.5 are under development, as is the C-terminal approximately 500 amino acids of the UL36 protein. Genes predicted to be in-frame subsets of longer polypeptides were not included, but this will not lead to loss of potential epitopes. A poorly studied variable is allelic heterogeneity in HLA class I assembly with Chlorocebus sp. β2m in Cos-7 cells. We overexpressed HSV-1 ORFs in isolation in aAPCs, where intracellular trafficking and class I presentation could differ from the viral context. There were subtle differences in some of our HLA-C constructs from the HLA-A and -B vectors, but our method has achieved excellent HLA-C expression (66). There are interactions between HSV-1 proteins such as proteolysis and phosphorylation (1), and possibly species-specific host protein–HSV-1 protein interactions, that would differ between infected and transfected cells. In HSV-2 work using a genomic DNA library and Cos-7 transfection, we decoded the fine specificity of each CD8 clone studied (52, 56, 67) and therefore believe such situations are rare for HSV. We focused on IFN-γ readouts of CD8⁺ T cell activation and proliferation to detect CD4⁺ T cell responses. With regard to effector cytokines, rare HSV-reactive T cells in PBMCs making TNF-α or IL-2 but not IFN-γ have been described (54). In preliminary studies, substitution of TNF-α for IFN-γ ELISA did not uncover additional specificities (data not shown). We noted one HSV-seronegative individual with CD8 responses to HSV-1 (participant 13 in Table 2). Further work will be required to determine whether reactivity can be confirmed at the epitope level, as has been done for HSV-2 (68).

We have extended the use of CD137 as an activation marker to two complex microbes for both CD4⁺ and CD8⁺ T cells. CD137 mediates a strong co-stimulatory signal to T cells. Thus, use of anti-CD137 to detect and purify antigen-reactive cells may assist their downstream expansion. Our data are consistent with some level of bystander CD137 expression, as the level of reactivity with whole HSV-1 among expanded CD137^hi cells varied between 4% and 45%. Enrichment was better for CD4 cells. We cannot be sure that all memory HSV-reactive cells upregulated CD137. CD137 is similar in this regard to other molecules used for enrichment, such as CD134, CD154, and captured IFN-γ (69).

In summary, the T cell response to a complex and serious pathogen with a large genome, HSV-1, has been decoded with a linked set of cellular and molecular tools to reveal novel candidate vaccine antigens. We have preliminarily identified the proteins encoded by genes UL39 and UL46 as having high population prevalence of coordinated CD8 and CD4 responses and plan to study larger, defined populations to refine these conclusions. Cross-presentation followed by CD137-based selection also effectively enriches rare CD8⁺ cells specific for vaccinia virus, an effective live virus vaccine. CD137 is also suitable for enrichment of CD4⁺ T cells reactive with whole microbe preparations, as demonstrated for both HSV-1 and vaccinia virus. Our flexible gene cloning format allows integrated, efficient study of both CD8 and CD4 responses after one round of PCR-based cloning of microbial ORFs. Use of appropriate initial re-stimulation conditions, CD137 as a flexible selection marker, and the genomes and complete genome-covering ORF sets now available for Mycobacterium tuberculosis, Plasmodium falciparum, and other agents should speed comprehensive definition of T cell responses and vaccine design.

View Supplemental data

We gratefully acknowledge the participation of research participants with HSV infection at the University of Washington Virology Research Clinic. The clinical and regulatory staff at the Clinic provided invaluable assistance in obtaining the clinical specimens. The Virology Laboratory at Children’s Medical Center, Seattle, Washington, performed HSV type-specific serology. HIV-1 serology was done at the University of Washington. We thank M. Juliana McElrath and the HIV Vaccine Trials Network and the AIDS Clinical Trial Group for cell sorter help. We thank Joseph Blattman for help with fluorescence microscopy and flow cytometry. We thank Phil Felgner and D. Huw Davies for F. tularensis molecular clones. We thank Amanda Paulovich for use of equipment. We thank Stanley R. Riddell for assisting with the HLA C cDNA clones. Funding was provided by NIH grants AI30731, AI094019, AI081060, AI042528, BayGene (Bayerisches Staatsministerium für Wissenschaft, Forschung, und Kunst; J. Haas), the Deutsche Forschungsgemeinschaft (DFG; SFB 576, BA 1165/5-1), and the Medical Research Council (MRC; G0501453). We thank the James B. Pendleton Charitable Trust for purchase of a BD FACSAria flow cytometer cell sorter. Support was also provided by the Bill and Melinda Gates Foundation via the Poxvirus T Cell Vaccine Discovery Consortium (PTVDC) within the Collaborative AIDS Vaccine Discovery (CAVD) program.

Address correspondence to: David M. Koelle, 1616 Eastlake Avenue East, Suite 500, Seattle, Washington 98102, USA. Phone: 206.667.6491; Fax: 206.667.7711; E-mail: viralimm@u.washington.edu.

Conflict of interest: David M. Koelle has received consulting fees from Immune Design Corp. and research support from Coridon Pty Ltd. and Vical Inc. Anna Wald has received research funding and consulting fees from AiCuris.

Reference information: J Clin Invest. 2012;122(2):654–673. doi:10.1172/JCI60556.

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