Previous Article | Next Article ![]()
Infection and Immunity, January 2002, p. 79-85, Vol. 70, No. 1
0019-9567/01/$04.00+0 DOI: 10.1128/IAI.70.1.79-85.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Dipartimento di Biologia e Genetica per le Scienze Mediche, Università di Milano, 20133 Milan,1 Roche Milano Ricerche, 20132 Milan,2 Consorzio Antitubercolare "Istituto Villa Marelli," 20100 Milan,3 Azienda Ospedaliera "S. Maria degli Angeli," 33170 Pordenone,4 Cattedra di Chemioterapia, Università di Pavia, 27100 Pavia, Italy5
Received 16 July 2001/ Returned for modification 27 August 2001/ Accepted 16 October 2001
|
|
|---|
|
|
|---|
) (8, 11), as well as IFN-
receptor in humans (16, 23), were shown to be essential to the generation of a protective immune response to M. tuberculosis. Recently, depletion of CD4+ cells was shown to result in reactivation of latent M. tuberculosis infection in mice in spite of unaltered expression of IFN-
, suggesting that CD4+ cells could have roles in addition to IFN-
production in controlling M. tuberculosis infection (25). Therefore, the identification of antigens capable of eliciting CD4+ T-cell responses and the characterization of immunodominant T-cell epitopes are of primary importance for the development of subunit vaccines for tuberculosis. The role of CD8+ T cells in immunity to M. tuberculosis is less defined (10). CD8+ cytotoxic T cells capable of lysing infected macrophages as well as reducing the viability of intracellular mycobacteria through a granulysin-dependent mechanism were described (29). Moreover, epitopes from mycobacterial antigens capable of eliciting cytotoxic CD8+ T-cell responses were recently identified (17, 21, 6) as well as CD8+ T cells specific for mycobacterial antigens presented through an alternative major histocompatibility complex class I (MHC-I) processing pathway(s) (4, 19). MHC-II-restricted responses against M. tuberculosis have been more extensively characterized, and a number of M. tuberculosis antigens for CD4+ T cells have been identified to date. Recently, an immunodominant family of M. tuberculosis antigens recognized by T cells from healthy PPD (purified protein derivative)-reactive subjects was isolated (1). Expanding the knowledge of the human T-cell repertoire to peptide epitopes derived from M. tuberculosis antigens is also of potential interest for immunodiagnostic applications. Activation of CD4+ T cells is dependent upon the presentation of peptides from disease-related protein antigens in the context of MHC-II molecules. The MHC genes are the most polymorphic present in the genome of every species analyzed. Most of the differences in the products of individual MHC-II alleles are localized in the peptide binding groove and determine the peptide binding properties of the different MHC molecules. In this study, the products of the mycobacterial cell entry (mce) genes were submitted to analysis by T-cell epitope prediction software (TEPITOPE), which enables the computational identification of promiscuous and allele-specific HLA-DR ligands (31). The mce1 gene was originally defined as an element conferring invasiveness to a nonpathogenic strain of Escherichia coli (2). Moreover, an mce-deficient Mycobacterium bovis BCG mutant exhibited reduced ability to invade nonphagocytic cells (9). The analysis of the complete genome of M. tuberculosis revealed the existence of four mce gene homologues very similarly organized in operons containing eight genes (7). Five peptides predicted by TEPITOPE as potential HLA-DR ligands and based on the sequence of the Mce2 protein were tested for induction of proliferation of CD4+ cells isolated from M. tuberculosis-infected subjects bearing 12 different aplotypes. This analysis led us to the identification of a peptide inducing CD4+ cell proliferation in 50% of the tested subjects, indicating that the application of the TEPITOPE software to mycobacterial antigens could lead to the identification of promiscuous epitopes eliciting MHC-II-restricted responses during infection with M. tuberculosis.
|
|
|---|
T-cell epitope prediction. The sequences of the Mce proteins were subjected to HLA-DR ligand prediction by the TEPITOPE software to identify promiscuous HLA-DR ligands (13). We used a version of TEPITOPE incorporating 25 virtual matrices covering most of the human HLA class II peptide binding specificity in the Caucasian population. We set the TEPITOPE prediction threshold at 3% (31) and picked peptide sequences predicted to bind the most common HLA-DR alleles (DRB1*0101, DRB1*0301, DRB1*0401, DRB1*0701, DRB1*0801, DRB1*1101, and DRB1*1501). The peptides were chosen based on the predicted binding as well as the degree of similarity between the four mce members and were synthesized according to the sequence of the Mce2 protein. Peptide no. 4, which is present in two proteins and showed poor prediction of promiscuous binding, was used as a nonpromiscuous control.
Cloning, expression, and immunoblot of Mce2-Myc fusion protein with sera from M. tuberculosis-infected subjects. The mce2 gene was obtained from E. coli (NM554 strain) transformed with the cosmid MTCY19H5 (kindly provided by S. Cole) by PCR amplification with the following primers: forward 5'-CCATGGTGCCAACGCTGGTGACG and reverse 5'-AAGCTTTCATTAATTCAGATCCTCTTCTGAGATGAGTTTTTGTTCTGGGTTGATCGTGTTCTCTCC containing the sequence (underlined) encoding the c-myc-derived epitope. The mce-myc fragment was cloned in pCR2.1 (Invitrogen, Groningen, The Netherlands) that was used to transform Top 10 E. coli. Purified plasmid DNA was digested with HindIII and NcoI and cloned in pSE420 (Invitrogen) under the control of the trp-lac (trc) promoter. Isopropyl-ß-d-thiogalactopyranoside (IPTG) at 1 mM was used to induce the resulting transformants. The Mce2-Myc protein was selectively detected, by immunoblotting with an anti-Myc monoclonal antibody (MAb) in the subcellular fraction containing membranes and inclusion bodies of IPTG-induced transformants, as a band migrating with an apparent molecular mass of 45 kDa (not shown). To immunoprecipitate the Mce2-Myc protein, IPTG-induced bacteria were lysed in 1% sodium dodecyl sulfate (SDS) at 95°C for 20 min. After centrifugation at 20,800 x g for 15 min, the supernatant was diluted to 1:10 with 1% NP-40 in Tris-EDTA buffer and was immunoprecipitated with 9E10 anti-Myc MAb (CRL-1279; American Type Culture Collection) followed by Sepharose-coupled protein G. The immunoprecipitates were resolved in SDS-12% polyacrylamide gel electrophoresis under reducing conditions and were blotted onto nitrocellulose membranes. Immunoblots were performed with sera from M. tuberculosis-infected patients that were revealed by horseradish peroxidase-conjugated antibodies specific for human immunoglobulin G (IgG) and anti-Myc MAb as a control that was revealed by horseradish peroxidase-conjugated antibodies specific for mouse IgG. The enhanced chemiluminescence detection system (Amersham) was used to reveal the binding. Positive sera were reactive with the recombinant Mce2-Myc protein in Western blotting at 1:100 and 1:1,000 dilutions and were negative on anti-Myc-immunoprecipitated lysates from noninduced bacteria at 1:100 dilution.
DR peptide binding assay. The Mce2 peptides together with a control peptide derived from the sequence of Epithelial V-like antigen (12) were synthesized with a multiple peptide synthesizer (model 396; Advanced Chem Tech, Louisville, Ky.) using fluorenylmethoxycarbonyl chemistry and solid-phase synthesis. The ability of unlabeled Mce2-derived peptides to compete with a biotinylated indicator peptide was determined using an enzyme-linked immunosorbent assay (ELISA)-based competition assay, as described earlier (13). The following biotinylated indicator peptides were used: GFKA7 for DRB1*0101 (DR1) and DRB1*0701 (DR7), GIRA2YA4 for DRB1*1501 (DR2), IAYDA5 for DRB1*0301 (DR3), YPKFVKQNTLKA2 for DRB1*0401 (DR4), tetanus toxoid peptide 830-843 for DRB1*1101 (DR5), and GYRA6L for DRB1*0801 (DR8). The relative binding affinity of the predicted ligands for the different HLA-DR molecules was determined as the 50% inhibitory concentration (IC50) (i.e., the concentration of competitor peptide required to inhibit binding of the biotinylated indicator peptide by 50%) and was compared with the promiscuous HA307-319 peptide from influenza hemagglutinin.
Immortalization of autologous APCs and analysis of CD4+ T-cell response to Mce2 peptides. To immortalize autologous APCs, PBMCs isolated on a Ficoll density gradient were resuspended in RPMI 1640 medium (Gibco-BRL, Gaithersburg, Md.) supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 50 U of penicillin-streptomycin/ml, 50 nM ß-mercaptoethanol, 10% heat-inactivated fetal calf serum, 30% culture supernatant of the Epstein-Barr virus (EBV)-producing cell line B95.8 (generous gift of Paola Panina-Bordignon), and cyclosporine A (Novartis Pharma, Basel, Switzerland) at 300 to 600 ng/ml. After 3 days of culture, the supernatant was replaced with normal medium and cells were cultivated for 2 weeks. After an appropriate period of culture, cells were frozen. To analyze CD4+ T-cell responses to Mce2 peptides, PBMCs were resuspended at 106 cells/ml in complete RPMI 1640 medium supplemented with 10% human AB+ serum and 10 µg of whole-cell lysate of M. tuberculosis H37Rv (kindly provided by John T. Belisle, Colorado State University, Fort Collins, Colo.)/ml and cultivated for 3 days. Stimulated cells were expanded in medium with interleukin 2 (20 U/ml) to propagate T cells for stimulation with EBV-immortalized autologous B cells (27). Then 4 x 105 CD4+ T cells and 2 x 105 autologous, irradiated (6,000 rads) B cells were distributed in triplicate in 96-well plates and were stimulated with the various peptides at 1 and 10 µM concentrations. After 72 h, cell proliferation was assessed by [3H]thymidine incorporation and scintillation counting. The proliferative response was expressed as stimulation index (SI), the ratio between counts per minute of triplicate wells from CD4+ cells cultured with peptide and counts per minute for cells cultured without peptide. Cells displaying an SI/PPD-negative SI ratio of >2.5 were calculated to be significantly stimulated by a paired Student t test (P < 0.05).
|
|
|---|
![]() View larger version (74K): [in a new window] |
FIG. 1. Sequence alignment of Mce proteins. Shading indicates the peptides selected by TEPITOPE as ligands for the most common HLA alleles. The boxed peptides identified by the indicated numbers were synthesized and used in the HLA-DR-binding assay as well as the CD4+ T-cell proliferation assay.
|
|
View this table: [in a new window] |
TABLE 1. HLA-DR-binding assay of Mce2-derived peptidesa
|
![]() View larger version (16K): [in a new window] |
FIG. 2. (A) Western blots (WB) with human positive (+) and negative (-) sera as well as with anti-Myc MAb of anti-Myc immunoprecipitates from lysates of noninduced (NI) and IPTG-induced (I) E. coli transformants expressing the Mce2-Myc fusion protein. Heavy (H) and light (L) chains of the immunoprecipitating anti-Myc MAb as well as the Mce2-Myc protein (arrow) are indicated. Numbers on the right are molecular sizes in kilodaltons. (B) Relative distributions of M. tuberculosis-positive (black bars) and -negative (white bars) subjects with respect to IgG reactivity to Mce2-Myc protein in immunoblot.
|
![]() View larger version (10K): [in a new window] |
FIG. 3. (A) Relative representations of HLA-DR alleles in subjects tested for CD4+ T-cell proliferative responses. (B) Percentages of subjects responding to the different Mce2-derived peptides. (C) Correlation between percentages of proliferative responses obtained in the CD4+ T-cell stimulation assay and mean IC50s detected in the HLA-DR-binding assay with peptides 1, 2, 4, and 5.
|
![]() View larger version (28K): [in a new window] |
FIG. 4. Proliferative responses (expressed as ratio of SI of patient/SI of PPD-negative donor) to Mce2-derived peptides of typed patients with pulmonary tuberculosis. A paired Student t test was used to determine the P value that was <0.05 or <0.001 for cellular responses above the marked value of 2.5.
|
|
|
|---|
HLA-DR constitutes the dominant isotype of human MHC-II (33). TEPITOPE incorporates 25 virtual matrices covering the majority of human HLA-DR specificities and enables the systematic prediction of peptide ligands for a broad range of HLA-binding specificities (10). It was successfully employed to identify HLA-DR ligands derived from tumors (20, 31) and endogenous proteins involved in autoimmune diseases (14). We investigated whether promiscuous HLA-DR ligands could be identified in the sequences of the Mce protein family. We used a stringent threshold setting, which was proven to be effective in predicting up to 80% of an in vitro-selected peptide repertoire (31). The HLA-DR-binding assay with the five selected peptides corresponding to the Mce2 sequence confirmed the validity of such an approach. Indeed, peptides 2 and 3, which displayed the lowest IC50s, were predicted to be the most promiscuous ligands. Peptide 5 demonstrated high IC50s with most MHCs in spite of the promiscuous binding prediction, and this might be due to the high hydrophobicity of such a peptide. Nevertheless, we employed peptide 5 in the CD4+ T-cell proliferation assay, because it was shown that hydrophobic peptides could represent promiscuous T-cell epitopes and could be efficiently presented in vitro (26).
In vivo antigen processing and HLA class II binding are complex multistep processes that can be influenced by unpredictable mechanisms, i.e., the susceptibility to proteolysis of a given antigen, the specificity of the proteolytic enzymes involved during processing, and the stability of the generated peptides. We assessed the capacity of the selected peptides to be presented in vivo in the course of M. tuberculosis infection by testing the proliferation of CD4+ T cells from patients with pulmonary tuberculosis upon stimulation with autologous APCs loaded with the Mce2 peptides as well as a control, unrelated peptide. Such an analysis revealed that the percentage of proliferative responses was inversely correlated to the mean IC50 obtained in the HLA-binding assay. Peptide 3 displayed a significant increase in the percentage of proliferative responses with respect to the expected value by the correlation between mean IC50s and percentages of T-cell responses obtained with the other four peptides. This could be due to both the extended length with inclusion of more potential epitopes from the four Mce proteins and/or some preferential presentation of nonamers contained in peptide 3 to CD4+ cells in vivo. Two DRB1*04/08 patients did not respond to peptide 3 in the antigen presentation assay, whereas no restriction to particular aplotypes was evident in responses to peptide 2. Indeed, both DR4 and DR8 were not predicted to be optimal ligands for peptide 3 in the HLA-DR-binding assay, and peptide 2 displayed the most promiscuous pattern in such an assay.
The Mce proteins were predicted to bear signal sequences or hydrophobic stretches at the N terminus, suggesting that they could be either secreted or surface exposed (7), consistent with the proposed role of the Mce1 protein in invasion of host cells (2). The results presented in this study indicate that Mce proteins are immunogenic. Moreover, a promiscuous T-cell epitope could be identified by TEPITOPE in a region of homology of the four Mce proteins. Subunit vaccines consisting of mycobacterial protein antigens represent a potential safe and specific tool for the prevention of tuberculosis. A potential limit of subunit vaccines is limited persistence in vivo, resulting in the inability to induce strong primary responses with long-lived memory (18). However, it was recently shown that in mice previously immunized with BCG, memory CD4+ T cells could be boosted by a protein antigen (3). Since BCG is widely administered to children, immunization with BCG could be beneficial for obtaining more specific and protective secondary responses with subunit vaccines. The identification of promiscuous binding to HLA is an ideal prerequisite for the design of subunit vaccines. Since the complete genome of M. tuberculosis is available, TEPITOPE could constitute a valuable tool for the identification of immunogenic peptides from M. tuberculosis proteins selectively implicated in the various pathogenetic aspects of tuberculosis.
We thank Katharina Fleischhauer (Dibit-HSR, Milan, Italy) for HLA typing, Maria Guttinger (Dibit-HSR, Milan, Italy) and Paola Panina-Bordignon (Roche Milano Ricerche, Milan, Italy) for skillful advice on the T-cell proliferation assay, Massimiliano Tattanelli (Università di Milano) for help in cloning the Mce2-Myc protein, Luca Scorrano (Dana Farber Cancer Institute, Boston, Mass.) for linear regression graphics, Stewart T. Cole and Karin Eiglmeier (Institut Pasteur, Paris, France) for the MTCY19H5 cosmid, and John T. Belisle (Colorado State University) for H37Rv whole-cell lysate (NIH, NIAID Contract N01 AI-75320).
|
|
|---|
ß TCR+ cells by Mycobacterium tuberculosis via an alternate class I MHC antigen-processing pathway. J. Immunol. 162: 372379.
, yet succumb to tuberculosis. J. Immunol. 162: 54075416.
gene-disrupted mice. J. Exp. Med. 178: 22432247.
in resistance to Mycobacterium tuberculosis infection. J. Exp. Med. 178: 22492254.
-receptor deficiency in an infant with fatal bacille Calmette-Guerin infection. N. Engl J. Med. 335: 19561961.
-secreting CD8+ T lymphocytes specific for Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 95: 270275.
-receptor gene and susceptibility to mycobacterial infection. N. Engl. J. Med. 335: 19411949.
and nitric oxide synthase 2. J. Exp. Med. 192: 347358.
This article has been cited by other articles:
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Copyright © 2009 by the American Society for Microbiology. For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»