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The Journal of Immunology, 2004, 173: 1966-1977.
Copyright © 2004 by The American Association of Immunologists

Characterization of a Mycobacterium tuberculosis Peptide That Is Recognized by Human CD4+ and CD8+ T Cells in the Context of Multiple HLA Alleles1

Homayoun Shams2,*,{dagger}, Peter Klucar*, Steven E. Weis§, Ajit Lalvani, Patrick K. Moonan§, Hassan Safi*,{dagger}, Benjamin Wizel*,{dagger}, Katie Ewer, Gerald T. Nepom||, David M. Lewinsohn#, Peter Andersen** and Peter F. Barnes*,{dagger},{ddagger}

* Center for Pulmonary and Infectious Disease Control, and Departments of {dagger} Microbiology, Immunology, and {ddagger} Medicine, University of Texas Health Center, Tyler, TX 75708; § Department of Internal Medicine, University of North Texas Health Science Center, Fort Worth, TX 76107; Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom; || Benaroya Research Institute, Seattle, WA 98101; # Division of Pulmonary and Critical Care Medicine, Oregon Health and Science University/Portland Veterans Affairs Medical Center, Portland, OR 97207; and ** Statens Seruminstitut, Copenhagen, Denmark


    Abstract
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
The secreted Mycobacterium tuberculosis 10-kDa culture filtrate protein (CFP)10 is a potent T cell Ag that is recognized by a high percentage of persons infected with M. tuberculosis. We determined the molecular basis for this widespread recognition by identifying and characterizing a 15-mer peptide, CFP1071–85, that elicited IFN-{gamma} production and CTL activity by both CD4+ and CD8+ T cells from persons expressing multiple MHC class II and class I molecules, respectively. CFP1071–85 contained at least two epitopes, one of 10 aa (peptide T1) and another of 9 aa (peptide T6). T1 was recognized by CD4+ cells in the context of DRB1*04, DR5*0101, and DQB1*03, and by CD8+ cells of A2+ donors. T6 elicited responses by CD4+ cells in the context of DRB1*04 and DQB1*03, and by CD8+ cells of B35+ donors. Deleting a single amino acid from the amino or carboxy terminus of either peptide markedly reduced IFN-{gamma} production, suggesting that they are minimal epitopes for both CD4+ and CD8+ cells. As far as we are aware, these are the shortest microbial peptides that have been found to elicit responses by both T cell subpopulations. The capacity of CFP1071–85 to stimulate IFN-{gamma} production and CTL activity by CD4+ and CD8+ cells from persons expressing a spectrum of MHC molecules suggests that this peptide is an excellent candidate for inclusion in a subunit antituberculosis vaccine.


    Introduction
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Eight million new cases and 1.8 million deaths annually worldwide are attributed to Mycobacterium tuberculosis, one of the leading causes of death from a single infectious agent (1). The burgeoning epidemic of HIV infection in regions where tuberculosis is common has created a growing population of persons that are highly susceptible to M. tuberculosis. In addition, the continued spread of multidrug-resistant tuberculosis threatens to overwhelm the public health capacity of many jurisdictions (2, 3). These unfavorable factors will cause tuberculosis to remain a major health problem in the coming decades, and increase the urgency for development of an effective vaccine.

The only available antituberculosis vaccine is bacillus Calmette-Guérin (BCG),3 a live attenuated Mycobacterium bovis that was created in 1921. Vaccination with M. bovis BCG reduces the severity of tuberculosis in children, but does not protect against development of tuberculosis. Furthermore, vaccination can cause life-threatening disease in immunocompromised patients, such as those with HIV infection (4).

T cells play a pivotal role in protection against tuberculosis, and many studies have shown that CD4+ T cells are essential for immunity (5). A growing body of evidence in animals and in humans suggests that CD8+ cells also contribute significantly to immune defenses against tuberculosis through lysis of infected cells, production of IFN-{gamma}, and direct microbicidal activity (6, 7, 8, 9, 10, 11, 12). Therefore, the most effective vaccine is likely to be one that elicits responses by both CD4+ and CD8+ T cells (12).

Most published evidence indicates that secreted M. tuberculosis Ags stimulate protective immunity (13). Two important secreted proteins are 6-kDa early secretory antigenic target (ESAT-6) and 10-kDa culture filtrate protein (CFP10), which form a tightly bound 1:1 heterodimeric complex (14). The encoding genes are cotranscribed (15) and are part of the RD1 region of the M. tuberculosis genome, which is deleted from M. bovis BCG. Restoration of RD1 enhanced the capacity of BCG vaccination to protect mice against subsequent infection with M. tuberculosis (16).

ESAT-6 and CFP10 stimulate T cells to produce IFN-{gamma} and exhibit CTL activity in animal models and in humans infected with M. tuberculosis, making them excellent candidates for inclusion in an antituberculosis subunit vaccine (17, 18, 19, 20). T cells from a high percentage of persons with latent tuberculosis infection recognize ESAT-6 and CFP10 (20, 21), suggesting that they either contain multiple epitopes that are restricted by different MHC molecules, or epitopes that are promiscuously recognized in the context of multiple MHC molecules. Several epitopes for CD4+ and CD8+ T cells, restricted by different MHC molecules, have been identified in ESAT-6, providing an explanation for its widespread recognition (18, 22, 23). In contrast, only two CD8 epitopes for CFP10 have been identified (24). In this study, we wished to determine the molecular basis for the recognition of CFP10 by most individuals with latent tuberculosis infection. We identified and characterized a 15-mer peptide of CFP10 that elicited IFN-{gamma} production and CTL activity by both CD4+ and CD8+ T cells from the majority of persons with latent tuberculosis infection, including those expressing several different MHC class I and class II molecules.


    Materials and Methods
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Study subjects

This study was approved by the Institutional Review Boards of the University of North Texas Health Science Center (Fort Worth, TX) and the University of Texas Health Center (Tyler, TX). Blood was obtained from 10 healthy tuberculin-negative donors without prior contact with tuberculosis patients, and from 132 donors who were recent contacts of patients with pulmonary tuberculosis. Seventy-six (58%) donors were Hispanic, 29 (22%) were white non-Hispanic, 21 (16%) were African American, and 6 (5%) were Asian. All donors had no symptoms of tuberculosis with normal chest radiographs. Donors were classified as having latent tuberculosis infection if they had a tuberculin skin test showing at least a 5-mm diameter of induration and their PBMC produced IFN-{gamma} in response to CFP10 or ESAT-6, based on the ELISPOT assay.

Peptides

We selected 15-mer peptides that overlapped by 10 aa and spanned the CFP10 protein. Truncated peptides were also synthesized, as outlined in the results. Peptides were synthesized by the Molecular Genetics Instrumentation Facility at the University of Georgia (Athens, GA) and by Invitrogen Life Technologies (Carlsbad, CA), using Fmoc chemistry. Peptide purity was >70%, as assayed by HPLC, and their composition was verified by mass spectrometry. Lyophilized peptides were dissolved at 25 mg/ml in DMSO, aliquoted, and stored at 4°C.

Antibodies

We used Abs to framework MHC class I (ATCC clone W6/32; American Type Culture Collection (ATCC), Manassas, VA) and MHC class II (ATCC clone 9.3F10; ATCC).

Isolation of PBMC and cell subpopulations

PBMC were obtained by centrifugation over Ficoll-Paque (Pharmacia, Uppsala, Sweden) and cultured in RPMI 1640 (Invitrogen Life Technologies, Gaithersburg, MD), supplemented with 10% heat-inactivated human AB serum (Atlanta Biologicals, Norcross, GA). In some experiments, CD4+, CD8+, or CD14+ cells were isolated from PBMC by positive selection with magnetic beads conjugated to the appropriate Abs (Miltenyi Biotech, Auburn, CA). Positively selected cells were >95% pure, as determined by flow cytometry.

Measurement of the frequency of IFN-{gamma}-producing cells

To measure the frequency of cells in PBMC that produced IFN-{gamma} in response to mycobacterial Ags or peptides, 2 x 105 cells per well were cultured in RPMI 1640 and 10% heat-inactivated human AB serum, with purified protein derivative (1 µg/ml; Statens Seruminstitut, Copenhagen, Denmark), CFP10 (10 µg/ml; Lionex, Braunschweig, Germany), ESAT-6 (10 µg/ml; Statens Seruminstitut) or CFP peptides (10 µg/ml) for 16–20 h in 96-well plates that were precoated with 15 µg/ml anti-human IFN-{gamma} mAb (1-DlK; Mabtech, Nacka, Sweden).

To measure the frequency of IFN-{gamma}-producing CD4+ or CD8+ cells, PBMC were cultured in T-25 flasks at 1.5 x 106 cells/ml, in medium alone, or with peptide (10 µg/ml), or purified protein derivative (1 µg/ml) for 48–72 h. Preliminary studies showed that this period of stimulation yielded the maximum number of IFN-{gamma}+ cells. After 48–72 h, cells were washed three times, and one aliquot was placed on an anti-IFN-{gamma}-precoated ELISPOT plate for 16–20 h. From two other aliquots, CD4+ and CD8+ cells were positively selected and placed on an ELISPOT plate for 16–20 h.

ELISPOT plates were washed with PBS plus 0.05% Tween 20, and anti-human IFN-{gamma} mAb 7-B6-1 conjugated to alkaline phosphatase (Mabtech) was added as the detection Ab. After 90 min, the plates were washed and 5-bromo-4-chloro-3-indolyl phosphate/NBT substrate (Moss, Pasadena, MD) was added for 2–5 min or until spots appeared. The spots in air-dried plates were counted using a stereomicroscope. Responses were considered positive if the Ag-stimulated well contained a mean of at least five more spot-forming cells than the mean of the negative control wells, and the Ag-stimulated value was at least twice the mean of the negative control value (20).

In some experiments, freshly isolated CD4+ cells (25,000 cells/well) or CD4+ clones (100 cells/well) were cultured with transfected bare lymphocyte syndrome (BLS) cells (25,000 cells/well), expressing a single HLA molecule (25) as APCs on an ELISPOT plate for 16–20 h. The number of IFN-{gamma}-producing cells was determined, as outlined above.

Expansion of peptide-specific CTLs

PBMC were washed, resuspended in RPMI 1640 containing 10% human AB serum, 20 mM HEPES, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids (all from Invitrogen Life Technologies), 50 U penicillin (Sigma-Aldrich, St. Louis, MO), and 10 µg/ml peptide, and seeded in 24-well plates (BD Biosciences, San Jose, CA) at 3 x 106 cells/well. After 3 days, 100 U/ml recombinant human IL-2 (Proleukin; Chiron, Emeryville, CA) was added to each well. After 7 days, 3 x 106 peptide-pulsed irradiated (3300 rad) autologous PBMC and 100 U/ml IL-2 were added to each well. Six days later, effector cells were tested for CTL activity in a 51Cr release assay.

In some cases, positively selected CD4+ and CD8+ effectors were isolated from peptide-expanded short-term lines, using immunomagnetic beads. Purity of these cells was 95–99%, as assessed by flow cytometry.

Generation of peptide-specific T cell clones

Clones were generated by previously described methods (26, 27). Briefly, autologous dendritic cells were generated as described below (preparation of target cells), pulsed with peptide T1, irradiated, and cultured at 104 cells per well in 96-well round-bottom plates with 300 CD4+ T cells in each well. Wells that showed visible growth were tested for reactivity with peptide T1 by ELISPOT. IFN-{gamma}+ T cell clones were expanded with anti-CD3 mAb (OKT3; Ortho Biotech, Bridgewater, NJ), irradiated allogeneic PBMC, and an EBV-transformed B cell line lymphoblastoid cell lines (LCL).

Assessment of CTL activity

Target cells were autologous dendritic cells, generated by incubating positively selected CD14+ macrophages with IL-4 (10 ng/ml; R&D Systems, Minneapolis, MN) and GM-CSF (10 ng/ml; R&D Systems) for 5 day. Dendritic cells were either unstimulated, infected with M. tuberculosis H37Rv for 48 h, or pulsed with a peptide overnight.

Targets were labeled overnight with 100 µCi of Na251CrO4 (Amersham Life Science, Arlington Heights, IL) at 37°C. After extensive washing, they were suspended in complete medium containing 10% FBS, and 104 cells/well were added in triplicate to round-bottom 96-well plates, each well containing 6 x 105 effector cells, an E:T ratio of 60:1. Plates were centrifuged at 500 x g for 2 min, then incubated for 5 h at 37°C. Supernatants were collected (Skatron, Sterling, VA), and 51Cr release was expressed as the mean percent specific lysis, calculated as: 100 x ([experimental release – spontaneous release]/[maximum release – spontaneous release]). Net specific lysis was calculated by subtracting the percent specific lysis of unpulsed target cells from the percent specific lysis of peptide-pulsed or M. tuberculosis-infected target cells. Maximum and spontaneous release were determined in wells containing target cells only, with or without 2% Triton X-100, respectively. Spontaneous release was always <15% of maximum release.

MHC typing

DNA was extracted from PBMC, using Wizard Genomic (Promega, Madison, WI). Low resolution HLA typing was performed, using PCR with sequence-specific primers (Combi Tray; GenoVision, West Chester, PA). Briefly, DNA samples (30 ng/µl) were mixed with a master mix containing Taq polymerase (GenoVision), added into the plates containing sequence-specific primers and amplified by PCR. PCR products (10 µl) were electrophoresed on a 2% agarose gel containing ethidium bromide. MHC alleles were identified with the GenoVision version of HELMBERG-SCORE Virtual Sequencing software.


    Results
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Two CFP10 peptides elicit IFN-{gamma} production by T cells from most persons with latent tuberculosis infection

PBMC from 132 close contacts of patients with pulmonary tuberculosis were stimulated with the M. tuberculosis-specific proteins, CFP10 and ESAT-6, which have previously been used to identify persons with latent tuberculosis infection (20, 21, 23). The ELISPOT assay was used to identify IFN-{gamma}-producing cells. Fifty-three subjects were classified as having latent tuberculosis infection, based on having positive tuberculin skin tests and IFN-{gamma}-producing PBMC in response to either ESAT-6 or CFP10. Of these 53, 49 responded to CFP10.

To identify the regions of CFP10 that induced IFN-{gamma} production, we tested overlapping 15-aa peptides that spanned CFP10 (20). CFP1071–85 and CFP1076–90 were the most potent, and were recognized by 83 and 91% of responders, respectively (Fig. 1). CFP1071–85 and CFP1076–90 did not elicit IFN-{gamma} production by PBMC from 10 tuberculin-negative persons who had no history of contact with tuberculosis patients.



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FIGURE 1. Capacity of CFP10 peptides to stimulate IFN-{gamma} production by PBMC from persons with latent tuberculosis infection. PBMC from 49 CFP10-responsive persons were cultured overnight on IFN-{gamma} ELISPOT plates with 15-mer overlapping peptides spanning the CFP10 protein. The values shown are the percent of CFP10 responders that produced >7 IFN-{gamma}+ cells per 2.5 x 105 cells to each individual peptide. Unstimulated PBMC showed 0–2 IFN-{gamma}+ cells per 2.5 x 105 cells.

 
CFP1071–85 and CFP1076–90 elicit IFN-{gamma} production and CTL activity by CD4+ and CD8+ T cells

We stimulated PBMC from eight donors with CFP1071–85 and CFP1076–90. After 48 h, we obtained CD4+ and CD8+ cells by positive immunomagnetic selection, and cultured them on ELISPOT plates overnight. CFP1071–85 induced IFN-{gamma} production by PBMC from eight donors (mean 300 ± 124 (SE) IFN-{gamma}+ cells per 2.5 x 105 cells; Fig. 2A), by CD4+ cells from seven donors (mean 205 ± 86 IFN-{gamma}+ cells per 2.5 x 105 cells; Fig. 2B) and by CD8+ cells from eight donors (mean 173 ± 85 IFN-{gamma}+ cells per 2.5 x 105 cells; Fig. 2C). CFP1076–90 was recognized by PBMC from six donors (mean 320 ± 176 IFN-{gamma}+ cells per 2.5 x 105 cells; Fig. 2A), by CD4+ cells from seven donors (mean 146 ± 64 IFN-{gamma}+ cells per 2.5 x 105 cells; Fig. 2B), and by CD8+ cells from five donors (mean 121 ± 83 IFN-{gamma}+ cells per 2.5 x 105 cells; Fig. 2C).



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FIGURE 2. CFP1071–85 and CFP1076–90 stimulate production of IFN-{gamma} by PBMC. PBMC from eight CFP10-responsive individuals were stimulated with peptides CFP1071–85 and CFP1076–90 for 48 h. PBMC and positively selected CD4+ or CD8+ cells were then cultured overnight on IFN-{gamma} ELISPOT plates. Values shown are the means and SEM of triplicate wells. Unstimulated PBMC showed 0–2 IFN-{gamma}+ cells per 2.5 x 105 cells. A, B, and C show results for PBMC, CD4+ cells, and CD8+ cells, respectively.

 
To determine whether CFP1071–85 and CFP1076–90 elicited CTL activity, PBMC were cultured with either peptide for 7 days, then restimulated for another 6–7 days. This brief period reduced the likelihood of artifactual induction of peptide-responsive CTL. For four donors, PBMC showed net specific lysis ranging from 6 to 45% against peptide-pulsed autologous dendritic cells (Fig. 3A). CD4+ T cells isolated from restimulated PBMC showed similar levels of net specific lysis as PBMC (6–46%; Fig. 3B) and CD8+ T cells showed lower levels of lysis (1–27%; Fig. 3C). Recent studies show that M. tuberculosis-responsive CD8+ T cell clones are more potent CTL than CD4+ T cell clones, using a low E:T ratio and suboptimal peptide concentrations (28). The different results in our experimental system may be due to our use of short-term T cell lines as effectors, a high E:T ratio and high peptide concentrations. The precursor frequency of CD4+ CTL may also be higher than that of CD8+ CTL in peptide-stimulated PBMC.



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FIGURE 3. CTL activity of short-term T cell lines stimulated with CFP1071–85 and CFP1076–90. PBMC from four donors were stimulated with peptides CFP1071–85 and CFP1076–90 for 13–14 days. These short-term lines were used as effectors. Positively selected CD4+ or CD8+ cells from these lines were also used as effectors. Targets were autologous dendritic cells, either unpulsed or pulsed with relevant peptides. A, B, and C show results, using peptide-stimulated PBMC, CD4+ cells, and CD8+ cells as effectors, respectively. Values shown are the means and SEM of triplicate wells.

 
CFP1071–85 is recognized by donors expressing different HLA alleles

CFP1071–85 elicited IFN-{gamma} production by both CD8+ and CD4+ cells from most donors with latent tuberculosis infection, suggesting that it is recognized in the context of multiple MHC alleles. To evaluate these possibilities, we performed MHC typing of seven donors whose CD4+ and CD8+ cells produced IFN-{gamma} in response to CFP1071–85 (Table I). No single MHC class I or class II allele was shared between all donors. However, of these seven individuals, six expressed DQB1*03 and four expressed DRB1*04. This suggests that CFP1071–85 contains a single epitope that is recognized promiscuously in the context of multiple MHC molecules, or that it contains two or more epitopes, each restricted by different MHC molecules.


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Table I. HLA typing of donors whose T cells recognized CFP1071–85a

 
Identification of minimal T cell epitopes within CFP1071–85

To identify the epitopes in CFP1071–85, we first truncated 1–5 aa from the N terminus (T1-T5, Table II). We also used a motif-based algorithm (29) to identify additional sequences in CFP1071–85 that were predicted to bind with high affinity (score, >9) to 4–8 MHC class I alleles (T6-T8, Table II). Finally, we identified a peptide that was predicted to bind with high affinity to three MHC class I alleles (T9, Table II).


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Table II. Truncated peptides derived from CFP1071–85a

 
PBMC from six CFP1071–85-responsive donors were stimulated with peptides T1-T9, and the frequency of IFN-{gamma}+ cells was measured by ELISPOT (Table III). The 9-mer T6 and CFP1071–85 elicited comparable numbers of IFN-{gamma}+ cells for all donors. The 10-mer T1 yielded similar numbers of IFN-{gamma}+ cells as CFP1071–85 for four donors, and 20–60% fewer IFN-{gamma}+ cells for two donors.


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Table III. Capacity of truncated peptides to stimulate IFN-{gamma} production by PBMCa

 
To determine whether peptides T1 and T6 contain minimal epitopes, we deleted 1–2 amino acids from the N or C terminus of these peptides. Removal of a single amino acid from either end of both peptides markedly reduced IFN-{gamma} production by PBMC (Table IV).


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Table IV. Effect of truncation on the capacity of peptides T1 and T6 to elicit IFN-{gamma} production by PBMCa

 
Peptides T1 and T6 are presented by MHC class I and II molecules

To identify the restriction elements for peptides T1 and T6, we treated PBMC with anti-MHC class I, anti-MHC class II, or control Ab for 4 h before addition of peptide on the IFN-{gamma} ELISPOT plate. Neutralization of MHC class I reduced the mean number of T1- and T6-responsive IFN-{gamma}+ cells by 50% (T1, mean 119 ± 18 vs 51 ± 15 cells per 2.5 x 105 cells, p = 0.02; T6, mean 139 ± 26 vs 65 ± 14 cells per 2.5 x 105 cells, p = 0.04; Table V). Anti-MHC class II reduced the number of IFN-{gamma}+ cells by >90% (T1, mean 119 ± 18 vs 9 ± 5 cells per 2.5 x 105 cells, p = 0.0001; T6, mean 139 ± 26 vs 8 ± 2 cells per 2.5 x 105 cells, p = 0.0005; Table V). Isotype control Abs had no effect on the number of IFN-{gamma}+ cells (data not shown).


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Table V. Effect of Abs to MHC class I and MHC class II on peptide-induced IFN-{gamma} production by PBMCa

 
Peptides T1 and T6 elicit IFN-{gamma} production and CTL activity by CD4+ and CD8+ T cells

PBMC from four donors were stimulated with peptides T1 and T6. Forty-eight to 72 h later, positively selected CD4+ and CD8+ cells were placed on an IFN-{gamma} ELISPOT plate. The frequency of peptide-responsive IFN-{gamma}+ cells was similar in CD4+ cells and PBMC (Fig. 4, A and B). The number of IFN-{gamma}+ CD8+ cells was lower than that of CD4+ cells, but higher than corresponding values for unstimulated cells in three donors for peptide T1 and four donors for peptide T6 (Fig. 4C).



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FIGURE 4. Peptides T1 and T6 stimulate production of IFN-{gamma} and CTL activity. PBMC from four donors were stimulated with peptides T1 and T6 for 48 h, and then PBMC (A) and purified CD4+ (B) and CD8+ T cells (C) were cultured overnight on IFN-{gamma} ELISPOT plates. Values shown are the means and SEM of triplicate wells. Unstimulated cells showed 0–2 cells per 2.5 x 105 PBMC. PBMC from five donors were cultured with peptides T1 or T6 for 13–14 days. These short-term lines (D), or positively selected CD4+ (E) or CD8+ cells (F) from these lines, were used as effectors. Targets were autologous dendritic cells, either unpulsed or pulsed with relevant peptides. Values shown are the means and SEM of triplicate wells.

 
We next evaluated the ability of peptides T1 and T6 to elicit CTL activity. PBMC from five donors were cultured with peptides T1 and T6 for 7 days and restimulated with peptide for 6–7 more days. PBMC effectors lysed autologous peptide-pulsed target cells (T1, net specific lysis 8–22%; T6, net specific lysis 6–17%; Fig. 4D). Positively selected CD4+ T cells showed similar results (T1 and T6, net specific lysis 8–39% and 8–20%, respectively; Fig. 4E). CD8+ T cells also lysed comparable numbers of peptide-pulsed autologous target cells. However, because CD8+ cells lysed a high percentage of unpulsed targets, net specific lysis was relatively low (T1, 2–14%; T6, 4–10%; Fig. 4F).

Dendritic cells infected with M. tuberculosis express peptides T1 and T6

To determine whether peptides T1 and T6 are expressed by APCs during M. tuberculosis infection in vivo, we cultured PBMC from three donors with T1 and T6, and tested their capacity to lyse autologous dendritic cells infected with H37Rv. T1-primed effector PBMC and CD4+ cells showed modest lytic activity (net specific lysis 7–13%; Fig. 5, A and C). T6-primed effector PBMC and CD4+ cells lysed infected cells from two of three donors (net specific lysis 0–32%; Fig. 5, B and D). CD8+ effector cells pulsed with T1 or T6 also lysed infected dendritic cells, but nonspecific lysis was higher than for CD4+ cells (net specific lysis 2–32%; Fig. 5, E and F).



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FIGURE 5. CTL activity of effector cells stimulated with peptides T1 and T6 against M. tuberculosis-infected target cells. PBMC from three donors were cultured with peptides T1 (A, C, and E) or T6 (B, D, and F) for 14 days. These short-term lines, and positively selected CD4+ or CD8+ cells from these lines, were used as effectors. Targets were autologous dendritic cells, either uninfected or infected with H37Rv. Means and SEM of triplicate wells are shown. Effectors used in A and D are peptide-stimulated PBMC, effectors in B and E are CD4+ cells, and those in C and F are CD8+ cells.

 
MHC restriction of T cells that recognize peptides T1 and T6

All nine donors whose T1- or T6-primed CD4+ T cells exhibited CTL activity or produced IFN-{gamma} expressed DQB1*03, and seven of nine also expressed DRB1*04 (Table VI). All five donors whose T1-primed CD8+ T cells showed CTL activity or IFN-{gamma} production were HLA A*02+, whereas all five donors whose T6-primed CD8+ T cells showed CTL activity or IFN-{gamma} production were HLA B*35+. Three donors whose CD8+ T cells responded to T1 and T6 expressed both HLA A*02 and B*35 alleles.


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Table VI. HLA typing results and responses of CD4+ and CD8+ T cells to peptide T1 and peptide T6a

 
To more definitively demonstrate that peptides T1 and T6 are restricted by DRB1*04 and DQB1*03, we used transfected BLS cells expressing a single HLA allele as target cells. Freshly isolated CD4+ T cells were obtained from five persons who responded to CFP10 and were infected with M. tuberculosis, and from three uninfected persons who did not respond to CFP10. CD4+ cells from the CFP10-responsive donors produced IFN-{gamma} specifically in response to DRB1*0401+ or DQB1*0302+ targets pulsed with peptide T1 or T6, but not to unpulsed targets. In contrast, CD4+ cells from CFP10-negative donors did not produce IFN-{gamma} in response to peptide-pulsed targets (Table VII).


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Table VII. Presentation of peptides T1 and T6 by APC expressing a single HLA allelea

 
The results above suggest that peptides T1 and T6 are recognized in the context of more than one MHC class II allele. To confirm these findings at the level of the single cell, we used two T1-specific CD4+ T cell clones as effector cells. BLS cells lacking endogenous MHC class II expression (BLS-1) and six BLS cell lines, each expressing a single transfected HLA class II allele, were used as APCs. Significant numbers of IFN-{gamma}+ cells were only observed in the presence of peptide, and BLS cells alone elicited IFN-{gamma} production by ~10% of the clones (Fig. 6). The frequency of IFN-{gamma}+ cells in both clones was 3- to 6-fold higher when BLS cells expressing DRB5*0101 or DRB1*0401 were used, and BLS cells expressing DQB1*0602 yielded a 2-fold higher response by clone B9. Cells expressing DRB1*0401 induced the strongest response in both clones.



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FIGURE 6. Peptide T1 is recognized by T cell clones in the context of different HLA class II alleles. T1-responsive clones B9 and F10 were generated from a donor whose MHC class II alleles were DQB1*03, DQB1*02, DRB1*04, and DRB1*07. Thirty-five percent and 58% of B9 and F10 cells produced IFN-{gamma} in response to T1-pulsed autologous macrophages, respectively. Clones were incubated with BLS cells lacking endogenous MHC class II alleles, and with BLS cells expressing single HLA class II alleles, in the presence or absence of peptide at concentrations of 10, 1, and 0.1 µg/ml. Clones without BLS cells were also used as controls. A total of 25,000 BLS cells and 100 clones were placed into each well in duplicate, and the number of IFN-{gamma}-producing cells was enumerated after 16 h. Values shown are the mean of duplicate results obtained with a peptide concentration of 1 µg/ml. A total of 10 µg/ml peptide yielded essentially identical results. The number of IFN-{gamma}+ cells was reduced by >90% when the peptide concentration was 0.1 µg/ml.

 

    Discussion
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Based on data using purified CD4+ and CD8+ primary T cells, T cell lines, and T cell clones, we demonstrated that a 15-mer peptide in the secreted mycobacterial protein CFP10 elicits IFN-{gamma} production and CTL activity by both CD4+ and CD8+ T cells from a high proportion of persons with latent tuberculosis infection. CFP1071–85 was recognized by CD4+ and CD8+ T cells from persons expressing multiple MHC class II and class I molecules, respectively (Table I), and contains at least two epitopes, one of 10 aa (peptide T1) and another of 9 aa (peptide T6). T1 was recognized by CD4+ cells in the context of at least DRB1*0401, DRB5*0101, and DQB1*0302, and by CD8+ cells of A2+ donors (Tables VI and VII, and Fig. 6). T6 elicited responses by CD4+ cells in the context of DRB1*0401 and DQB1*0302, and by CD8+ cells of B35+ donors (Tables VI and VII). Deleting a single amino acid from the amino or carboxy terminus of either peptide markedly reduced IFN-{gamma} production, suggesting that they are minimal epitopes for both CD4+ and CD8+ cells. As far as we are aware, these are the shortest microbial peptides that are known to stimulate responses by both T cell subpopulations. The capacity of CFP1071–85 to stimulate IFN-{gamma} production and CTL activity by CD4+ and CD8+ cells from persons expressing a spectrum of MHC molecules suggests that this peptide is an excellent candidate for inclusion in an antituberculosis vaccine.

CD4+ and CD8+ T cells play complementary roles in protective immunity to many intracellular pathogens, including M. tuberculosis. CD4+ cells are the major source of the macrophage-activating factor IFN-{gamma}, whereas CD8+ cells predominate in lysing infected cells (28). CD4+ cells also enhance the CD8+ cell response to Ag through interactions between CD40L on the surface of CD4+ cells and CD40 on APCs and on CD8+ cells (30, 31, 32), and we have recently shown that the CD40/CD40L pathway contributes significantly to the human CD8+ T cell response to M. tuberculosis (33). To maximize the protective immune response, it is theoretically appealing to vaccinate with peptides that contain epitopes for both CD4+ and CD8+ T cells. Such peptides can be presented by the same APC to both T cell subpopulations, and their close physical proximity may favor CD40/CD40L interactions and cytokine effects that enhance CD8+ cell effector function. Administration of a peptide containing a CTL epitope of HIV fused to a Th epitope yielded increased CTL responses (34), and vaccination with a 35-mer peptide containing both a CTL and a Th epitope of human papillomavirus completely eradicated papilloma virus-expressing tumors in a murine model (35).

Although epitopes for CD4+ cells and those for CD8+ cells can be fused to create chimeric peptides, naturally occurring peptides recognized by CD4+ and CD8+ cells may elicit more effective immunity because they are more likely to undergo appropriate Ag processing. Fused peptides can also create junctional epitopes that inhibit the immune response to the desired epitopes (36). An epitope comprising 15 aa capable of binding to both MHC class I and class II molecules in a murine model has been identified for HIV (37) and CD8 epitopes within CD4 epitopes are present in Plasmodium falciparum (38). CD8 epitopes of P. falciparum that were nested within CD4 epitopes were more antigenic for humans than other CD8 epitopes, supporting the enhanced immunogenicity of peptides that stimulate both classes of T cells.

Peptides within the M. tuberculosis proteins Ag 85B, ESAT-6, mce2, and the 16-kDa proteins MPB70 and {alpha}-crystallin are recognized by T cells from persons expressing more than one MHC class II haplotype (39, 40, 41, 42, 43, 44). In most of these studies, peptides of 16–25 aa were studied, minimal epitopes were not delineated by peptide truncation, or responses of purified CD4+ cells were not tested (39, 40, 41, 42, 43). Therefore, these peptides may contain more than one CD4 epitope, or a CD4 and CD8 epitope, rather than a single promiscuous CD4 epitope. Valle and colleagues identified a 12-aa peptide of Ag85 that elicited proliferation by PBMC from 89% of healthy tuberculin reactors (44). However, because a proliferative response was defined as only 2-fold that of background levels, and MHC typing of the donors was not performed, it is uncertain whether this peptide is truly promiscuous. The current study provides the most definitive evidence to date that M. tuberculosis peptides of only 9–10 aa can be recognized by persons expressing multiple MHC class II alleles. These peptides are shorter than the 13–16 aa peptides that have generally been found to bind MHC class II molecules.

Anti-MHC class I reduced the number of peptide T1- and T6-responsive IFN-{gamma}+ cells by ~50%, whereas anti-MHC class II almost completely abrogated the response (Table V). These results suggest that MHC class I-restricted CD8+ T cells contribute significantly to IFN-{gamma} production induced by M. tuberculosis peptides. However, this response depends on the presence of CD4+ cells. These findings extend the results of prior studies indicating that the capacity of CD8+ T cells to produce IFN-{gamma} in response to heat-killed M. tuberculosis requires CD4+ cells, probably through CD40/CD40L interactions (33, 45).

CFP10 is recognized by T cells from the majority of persons with latent tuberculosis infection and by persons with active tuberculosis, including patients with HIV infection (20, 46, 47). The carboxy end of the molecule is highly immunogenic, and peptides 71–90 elicit responses by 30–50% of PBMC from CFP10-responsive persons in Zambia and India (20, 46). The current results confirm and extend these findings, demonstrating that CFP1071–85 contains at least two epitopes for CD4+ T cells, and is recognized in the context of DRB1*0401, DRB5*0101, and DQB1*0302 (Tables VI and VII, and Fig. 6). The responsiveness of CD4+ T cells from subject T225 to the CFP10 peptides in the absence of DRB1*04 or DQB1*03 (Table I) may be due to the expression of DRB5*0101, which is linked to the DRB1*1501 allele in HLA-DR2+ subjects. Peptide T1 contains isoleucine at position 1, alanine at position 4, and valine at position 6, conforming to the motif predicting strong binding to HLAB1*0401, which is the most common subtype of HLAB1*04 in the United States (48). In contrast, peptide T6 shows no features of this motif. Because some donors whose CD4+ T cells produced IFN-{gamma} in response to CFP1071–85 expressed other MHC class II alleles (Table I, and data not shown), peptides T1 and T6, or other epitopes on CFP1071–85, are likely to be presented by additional class II molecules. Our findings are consistent with previous work demonstrating that certain peptides can bind to at least seven common DR types, including DRB1*0401 (49).

Previous work has shown that CFP1085–94 and CFP102–11 are HLA-B14- and HLA-B44-restricted epitopes, respectively, for human CD8+ T cell clones (24). We found that CFP1071–85 contains at least two epitopes for CD8+ T cells, one recognized by persons expressing HLA-A*02 and the other by persons expressing HLA-B*35 (Table VI). CD8+ T cells from persons expressing other MHC class I alleles may also recognize these epitopes, as formal restriction analysis with cells expressing a single allele was not performed. HLA-A*02 is part of the HLA-A2 supertype, which is expressed by 39–46% of Caucasians, North American Blacks, Hispanics, and Asians (50). HLA-B*35 is part of the HLA-B7 supertype, which is expressed by 43–57% of these ethnic groups. Therefore, CFP1071–85 is likely to be recognized by CD8+ T cells from the majority of people in different populations throughout the world.

The capacity of CFP1071–85 to elicit IFN-{gamma} production and CTL activity by CD4+ and CD8+ T cells from persons bearing multiple MHC class I and class II alleles makes it an intriguing candidate for inclusion in an antituberculosis vaccine. DNA vaccines encoding short peptides or peptide-based vaccines are attractive because they are substantially easier to produce than vaccines based on whole proteins. In addition, epitopes in proteins that elicit suppressive or immunopathogenic responses can be avoided. Peptides such as CFP1071–85, perhaps in combination with other immunodominant M. tuberculosis peptides, may also be useful to develop a diagnostic test for latent tuberculosis infection, based on an ELISPOT assay that detects IFN-{gamma}-producing cells. However, a vaccine that includes CFP1071–85 would limit the clinical utility of CFP1071–85-based diagnostic tests in the vaccinated population. These potentially contrasting roles will need to be reconciled in the future.


    Acknowledgments
 
We are grateful to Mabtech and Staffan Paulie for providing us with precoated IFN-{gamma} ELISPOT plates, and to Ortho Biotech for provision of anti-CD3 mAb. We thank Sharon Kochik for excellent technical assistance in handling BLS cells and transfectants.


    Footnotes
 
The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

1 This work was supported by grants from the National Institutes of Health (AI44935), the Cain Foundation for Infectious Disease Research, the Wellcome Trust, and the Center for Pulmonary and Infectious Disease Control. P.F.B. holds the Margaret E. Byers Cain Chair for Tuberculosis Research. A.L. is a Wellcome Senior Research Fellow in Clinical Science. Back

2 Address correspondence and reprint requests Dr. Homayoun Shams, Center for Pulmonary and Infections Disease Control, University of Texas Health Center, 11937 US Highway 271, Tyler, TX 75708. E-mail address: amir.shams{at}uthct.edu Back

3 Abbreviations used in this paper: BCG, bacillus Calmette-Guérin; BLS, bare lymphocyte syndrome; CFP, culture filtrate protein; ESAT, early secretory antigenic target. Back

Received for publication December 16, 2003. Accepted for publication May 24, 2004.


    References
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 

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H. Shams, S. E. Weis, P. Klucar, A. Lalvani, P. K. Moonan, J. M. Pogoda, K. Ewer, and P. F. Barnes
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Am. J. Respir. Crit. Care Med., November 1, 2005; 172(9): 1161 - 1168.
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