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Journal of Virology, June 2006, p. 5509-5515, Vol. 80, No. 11
0022-538X/06/$08.00+0 doi:10.1128/JVI.02659-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
,
Patrick McGowan,6,
,
Amalia Meier,1,5
David M. Koelle,1,2,3,4,7
Paul Sleath,6
Felecia Wagener,6
Mark Elliott,6
Ken Grabstein,6
Christine Posavad,2 and
Lawrence Corey1,2,4*
Departments of Laboratory Medicine,1 Medicine,2 Pathobiology, University of Washington, Seattle, Washington,3 Program in Infectious Diseases,4 Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, Washington,5 Corixa Corporation, Seattle Washington,6 Benaroya Research Institute, Seattle, Washington7
Received 19 December 2005/ Accepted 17 March 2006
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(This work was presented in part at the 28th International Herpesvirus Workshop, Madison, Wis., 2003 and the 27th International Herpesvirus Workshop, Cairns, Australia, 2002.)
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Preparation of PBMC from human subjects. Subjects were leukapheresed at the Puget Sound Blood Center. Peripheral blood mononuclear cells (PBMC) recovered from the leukapheresis product by Ficoll-Hypaque density gradient separation were washed thoroughly, suspended in 10% dimethyl sulfoxide (DMSO)/50% human serum/40% RPMI 1640, frozen at approximately 2.5 x 107 cells per cryovial, and stored in liquid nitrogen.
Preparation of DC. PBMC were suspended in RPMI plus 2% human serum (HS) and allowed to adhere to wells of six-well plates for 2 h at 37°C. Nonadherent PBMC were removed and transferred to a second six-well plate, and IL-4 (10 ng/ml) (gift from Immunex, Seattle, WA) and granulocyte-macrophage colony-stimulating factor (GM-CSF; 10 ng/ml) (gift from Immunex, Seattle, WA) were added. Dendritic cell (DC) culture medium (RPMI plus 5% fetal calf serum [FCS], 10 ng/ml IL-4, 10 ng/ml GM-CSF) was added to the first plate. Both plates were cultured at 37°C. The following day, nonadherent cells were removed from the second plate, DC medium was added, and the cells were returned to 37°C. DC were harvested from both plates after a total of 5 to 7 days and used as antigen-presenting cells (APC) in enzyme-linked immunospot (ELISPOT) assays.
Reagents. Human type AB serum (HS) was prepared by pooling and heat-inactivating serum from groups of 30 to 50 healthy donors. Cell culture medium consisted of RPMI 1640 (Gibco/BRL), 10% HS, 1 x 105 M 2-mercaptoethanol (Sigma, St. Louis, MO), 1 x 102 M HEPES (Invitrogen, Carlsbad, CA), 1 x 104 M sodium pyruvate (Invitrogen, Carlsbad, CA), 2 x 103 M glutamine (Invitrogen, Carlsbad, CA), and 50 µg/ml gentamicin (Invitrogen, Carlsbad, CA). Dithiothreitol (DTT; 2 x 104 M; Sigma) was added to the ELISPOT medium because sulfhydryl modification after storage in DMSO can significantly reduce the antigenicity of synthetic peptides (4). In preliminary experiments, DTT did not alter any aspect of ELISPOT assays other than significantly improving CD8 T-cell recognition of cysteine-containing epitopes (e.g., UL47/550; see below).
Selection of HSV-2 ORFs for study. Open reading frames (ORFs) for peptide synthesis (n = 48) were selected from among the known ORFs for HSV-2 (5) at the time the study was initiated (Table 1). Resource limitations necessitated selection of a subset of HSV-2 ORFs. Selection of ORFs was primarily based on published data suggesting human CD8 T-cell responses tend to be specific for immediate-early (IE) and virion proteins (capsid, tegument, and glycoprotein) (6, 7, 10, 11, 14, 19). Five additional ORFs (UL23, UL29, UL39, UL50, and UL55) were selected because they had been discovered, using expression-cloning methods, to be novel antigens recognized by HSV-specific CD4 T cells (9, 17; Hosken et al., unpublished).
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TABLE 1. Overlapping 15-mer peptides synthesized for this study
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Preparation of peptide pools. Peptide pools were prepared for each HSV-2 ORF from the individual peptide stocks by combining individual peptides so that each was present at 100 µg/ml in a final volume of 100 µl of DMSO. Peptide pools were stored in cryovials at 4°C. Two types of peptide pools were prepared: library pools and array pools. Library pools were prepared by grouping peptides linearly across an ORF (Table 1). The average library pool contained 50 peptides, a number which was shown to be optimal for detection of most CD8+ T-cell responses. Array pools were prepared by arranging the peptides within a single library pool in a row-and-column format and pooling the peptides in each column or row.
ELISPOT assay for detection of CD8+ T-cell responses. Because the purpose of the study was to define CD8 responses to HSV-2, purified CD8+ T cells were used as responders in ELISPOT assays. Preliminary experiments also showed that T-cell responses to previously known (6) CD8 epitopes (e.g., UL47/289 and UL47/551) were often at or below the limit of detection when whole PBMC were used, but were significantly above the limit of detection with purified CD8+ responder cells. The use of autologous dendritic cells and highly enriched CD8+ T cells reduces the ELISPOT assay background as compared to when whole PBMC are used (see below).
CD8+ T cells were prepared by positive selection using CD8+ Microbeads (Miltenyi, Auburn, CA) using MACS columns per the manufacturer's directions. T cells enriched by either positive or negative selection using magnetic beads gave identical responses to known CD8 T-cell epitopes in preliminary experiments. Positive selection was used because it yielded higher-purity CD8+ T cells, estimated at >95% in preliminary analyses as assessed by flow cytometry.
Peptides were screened by 24-h coculture of CD8+ T cells (5 x 105/well), autologous dendritic cells (5 x 104/well), and peptides in 96-well ELISPOT plates that had been precoated with anti-human gamma interferon (IFN-
) antibody 1D1K (mAbTech, Mariemont, OH). Each library pool was screened once. Each peptide in the pool was present at a final concentration of 0.5 µg/ml, which was determined in preliminary experiments to be optimal for detection of responses while minimizing false positives. ELISPOT plates were subsequently developed by sequential incubation with biotinylated 7-B6-1 monoclonal antibody (MAb) (mAbTech), Avidin-peroxidase (Vectastain ABC kit; Vector Labs, Burlingame CA), and AEC substrate (AEC kit; Vector Labs, Burlingame, CA). ELISPOTS were counted with an automated video-microscopy ELISPOT reader (Zeiss, Berlin, Germany). ELISPOTS from selected wells were also visually screened under a stereo microscope to verify the results.
Statistical methods.
Statistical analyses used SAS for Windows 9.1 (SAS Institute Inc., Cary, NC.). CD8 T-cell responses to HSV-2 proteins were analyzed both collectively and separately by ORFs. Each assay run utilized a single medium control. Each medium control (n = 40) had
8 spot-forming units (SFU)/106 CD8+ T cells. Their value was not utilized in analyses. The criterion for scoring an ORF as positive, chosen as an absolute number of SFU, was selected to minimize the number of samples from HSV-seronegative persons that produced a response above the cutoff. ORF-level CD8 T-cell responses were examined individually for ORFs found to be positive in at least 25% of HSV-2-seropositive participants. ORFs found to be positive in fewer than 25% of subjects were not evaluated individually. As assays were sometimes performed by dividing the complete ORF into two to seven segments, responses to each ORF were scored as positive when any of the segments were found to be positive. ELISPOT results were analyzed both as frequencies of subjects with positive responses, and as amino acid-adjusted frequency, where the proportion positive was divided by ORF length. Associations with participant-level characteristics were again tested using the chi-square test for frequencies and the Wilcoxon test for length-adjusted frequencies. Multiple-comparison techniques were used to adjust for the potential risk of false significance when testing many ORFs against each characteristic; specifically, the method of Benjamini and Hochberg was applied to control the false discovery rate of 5% per characteristic (2).
The collection of ORF-specific CD8 responses for each participant was graphically summarized using a magnitude-breadth curve. The magnitude-breadth curve for each participant plots the proportion of ORF-specific ELISPOT responses (net SFU/106 CD8 cells) larger than a threshold value, x, as a function of x; therefore, at each point the y axis indicates the average proportion of responses exceeding the response level designated on the x axis. A simple quantitative summary of the overall magnitude of each individual's CD8 response is computed as the area under the magnitude-breadth curve (AUC). The AUC value is equivalent to the average of the ORF-specific responses. To construct the curve, individuals are grouped by common characteristics and the proportions of each individual's responses that exceed a threshold are averaged within the group for each threshold. These average proportions are then plotted against the threshold and, for each group, connected by a line. Differences in this averaged response by other participant-level characteristics (HLA type, gender, etc.) were tested using the Wilcoxon rank sum test. Only HLA types present in at least 25% of subjects were considered.
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TABLE 2. Participant characteristics
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Figure 1a depicts the frequency of CD8+ T cell responses for all 37 HSV-2-seropositive persons. The number of subjects studied for each ORF varied as discussed above. The response rates varied from <5% to 70% of persons, with the highest frequency of responses (by ORF) to UL39, UL25, UL27, ICP0, UL46, UL47, UL19 U36, UL49, and UL26 in descending order of frequency. Responses to these ORFs ranged from 38% to 70% of the tested subjects. When categorized by functional group, 83% of the subjects developed a CD8+ T-cell response to a capsid protein, 83% to at least one tegument protein, 70% to an IE protein, and 45% to an envelope protein. The median number of ORFs to which an individual responded was 11 (range, 3 to 46; Fig. 2). The frequencies of the response were strongly correlated with the length of the ORF and hence the number of peptides utilized to cover an ORF (Spearman correlation statistic,
= 0.4, P < 0.001). As such, we also calculated an amino acid-adjusted response rate to each HSV-2 ORF. The amino acid-adjusted frequency of responses to the top ORFs were as follows in descending order: US9, UL11, UL35, US5, UL39, UL1, UL23, UL25, US6, and UL4 (Fig. 1b).
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FIG. 1. Frequency of CD8+ T-cell responses to HSV proteins among 37 subjects with HSV-2 infection. (a) Proportion of subjects with responses (defined as >20 SFU/106 CD8+ cells) to ORFs listed on the x axis. ORFs are organized by structural and functional categories. (b) CD8 responses adjusted for lengths of the predicted HSV-2 proteins. Amino acid (AA)-adjusted frequencies were computed by dividing the proportion of subjects with positive responses by the number of amino acids in the ORF.
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FIG. 2. Breadth of the CD8+ T-cell response to HSV-2. The number of ORFs to which positive ( 20 SFU/106 CD8+ T cells) responses were detected is plotted versus the number of responding subjects among the 21 HSV-2-seropositive subjects with genital herpes who were assayed against the complete set of peptides covering 48 HSV-2 ORFs.
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FIG. 3. Magnitude of the CD8+ T-cell response to HSV-2. Shown are cumulative CD8+ T-cell responses for 21 subjects to peptide pools covering 48 HSV-2 ORFs.
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responses to HSV peptides. These included A*01 (P = 0.66), A*03 (P = 0.27), B*44 (P = 0.40), C*01 (P = 0.37), C*03 (P = 0.57), and C*07 (P = 0.19). Nine persons with homozygous HLA class I A or B alleles had similar CD8+ T-cell responses to those heterozygous at both the A and B loci (P = 0.64). The 16 subjects with HSV-1 coinfection in addition to HSV-2 infection had similar overall magnitude of CD8 responses to those with HSV-2 infection alone (P = 0.92).
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FIG. 4. Magnitude-breadth curve representations of CD8 T-cell reactivity to HSV-2 peptide pools for subsets of HLA-defined subjects. (a) Comparison of HLA-A02 versus non-A02 subjects. (b) Comparison of HLA-B07 versus non-B07 subjects. (c) Comparison of HLA-A02 persons versus non-A02 subjects by class of HSV-2 proteins. (d) Comparison of HLA-B07 versus non-B07 by class of HSV-2 protein.
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We describe several novel findings about the human CD8 T-cell effector response to HSV-2. The diversity and breadth of this response are far greater than previously appreciated. The predominant CD8+ T-cell responses to HSV-2 are directed at IE, tegument, and capsid proteins within the set of 48 proteins we evaluated. Significant variations exist in the breadth of responses and reactivity to individual HSV-2 proteins between individuals. Some individuals demonstrate a low to moderate level of response (20 to 50 SFU/106) per ORF to many HSV-2 proteins, while others exhibit relatively high levels of response to few proteins and others modest responses to only one or two HSV-2 proteins. In addition, the magnitude and breadth of the CD8+ T-cell responses were influenced by HLA type in that persons with HLA A*02 appear to have a relatively lower response to HSV-2 than do people who do not have the HLA A*02 allele, while those with B*07 exhibited a higher frequency of responses to the peptides evaluated than persons who did not have HLA B*07.
Previous studies have reported a narrow diversity in the CD8 T-cell response to HSV. Previously described targets of the CD8 T-cell response include gB2, gD2, gE2, UL46, UL47, UL49, ICP0, ICP4, ICP22, ICP27, UL7, and UL25 (6, 10, 11, 14, 19, 20). Our study documented CD8+ T-cell responses to each of the 48 ORFs studied, expanding by threefold the ORFs to which CD8+ T-cell responses are directed. We have gained an initial insight into what might be the immunodominant and subdominant responses in human populations. It should be noted, however, that we have to date intensively studied only 21 persons and a much more extensive evaluation of a diverse group of persons with HSV-2 is needed before one can adequately characterize the response in human populations. In addition, the population we studied was overrepresented (3) in the frequency of those with HLA A*01, A*03, B*07, B*44, and C*01. Moreover, although our survey of 48 ORFs is more complete than previous studies, there are an additional approximately 30 ORFs that were not evaluated by us and require evaluation before a complete human CD8 T-cell response to HSV-2 can be measured.
As with all assays using peptides to define T-cell responses, the results are a function of the reagents used. The use of shorter peptides or different concentrations could influence the sensitivity and specificity of our assays. When ranking immunodominance between ORFs, we demonstrated a positive correlation between the length of the protein and the proportion of HSV-2-infected persons with positive responses. Hence, immunodominance may be influenced by the availability of peptides for binding to diverse HLA, as well as kinetic and cell biology considerations (23). Moreover, we based our peptides on the gene sequence of the HSV-2 HG52 strain, which is the only fully sequenced HSV-2 isolate in the public domain. While this isolate is derived from a patient with HSV-2 (5), we have recently undertaken sequencing of several of the ORFs from clinical isolates of the more frequently recognized proteins described herein. We clearly find mutations among isolates which can affect T-cell responses (12). Thus, it is likely that while our current study detects a large number of previously unknown responses, our data are likely an underestimation of the entire T-cell response to HSV-2. More complete responses can be defined with further refinement of peptides to the proteins we measured as well as the addition of the approximately 35 HSV-2 proteins we did not include in our study.
We used a novel ELISPOT strategy combining purified CD8+ responder cells and autologous dendritic cells as antigen-presenting cells. This provided clear differentiation between HSV-seronegative and HSV-2-seropositive persons, as shown by the low frequency of CD8+ responses in seronegative persons. As our initial goal was to pick up predominant responses, this was a useful strategy. However, this technique requires more blood volume than does the use of unfractionated PBMC as responder cells. Once we define immunologic responses, comparison with standard PBMC-based assays can be performed. Such an approach might be enhanced by optimizing the sensitivity of the immunogenic peptide pools.
One of the interesting features of our work is the diversity in the immune responses between individuals. This is especially seen in the magnitude-breadth curves. As the diversity of HSV-2 reactivation rates is also great (21, 22), our data suggest that studies defining the association between the magnitude and breadth of the CD8+ T-cell response to HSV-2 and viral reactivation can be performed. Studies to define the association between such responses and viral reactivation are approachable and appear warranted.
We thank Mark Alderson and Peter Probst (Corixa Corporation) and Louis Picker (University of Oregon) for technical advice and scientific discussion, Melody Smith for coordinating leukapheresis and HLA typing, and Karen Kinch for administrative oversight of grants.
Present address: ZymoGenetics Corporation, Seattle, Washington. ![]()
N.H. and P.M. contributed equally to the conception and conduct of this report. ![]()
Present address: Glaxo-Smithkline Biologicals Seattle, Seattle, Washington. ![]()
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