Computer-assisted prediction of HLA-DR binding and experimental analysis for human promiscuous Th1-cell peptides in the 24 kDa secreted lipoprotein (LppX) of Mycobacterium tuberculosis

Potential of a novel flagellin epitope as a broad-spectrum vaccine candidate against enteric fever

Relentless emergence of antibiotic resistant Salmonella strains, coupled with the drawbacks associated with currently available vaccines against enteric fever, warrants an urgent need to look for new vaccine candidates. Out of the multiple virulence factors harbored by Salmonella, flagella are regarded as one of the most important targets of innate as well as adaptive immune response. Individual Salmonella serotypes alternate between expression of two different antigenic forms encoded by fliC and fljB genes, respectively thereby employing this as a strategy to escape the host immune response. In the present study, using various immunoinformatic approaches, a flagellin epitope, present in both antigenic forms of typhoidal Salmonellae has been targeted. Following B-cell epitope and B-cell derived T-cell epitope prediction and interaction studies with major histocompatibility complexes using molecular docking, a peptide epitope was selected. Further, it was screened for its presence in majority of typhoidal serovars along with other useful attributes, in silico. Thereafter, safety studies were performed with the synthesized peptide. Subsequently, immunization studies were carried out using S. Typhi as well as S. Paratyphi A induced murine peritonitis model. Active immunization with peptide-BSA conjugate resulted in 75% and 80% mice survival following lethal challenge with S. Typhi and S. Paratyphi A respectively, along with a significant IgG antibody titer, thereby highlighting its immunogenic potential. Reduced bacterial burden in vital organs along with improved histoarchitecture and cytokine levels further substantiated the protective efficacy of the proposed candidate. Passive immunization studies with the candidate verified the protective efficacy of the generated antibodies against lethal challenge of bacteria in mice. Given the endemic nature of enteric fever and the antigenic variability observed in Salmonella serotypes, present study highlights the importance of using a vaccine candidate, which, along with generating a strong immune response, also exhibits a broad coverage against both, S. Typhi as well as S. Paratyphi A strains.

The role of immunoinformatics in the development of T-cell peptide-based vaccines against Mycobacterium tuberculosis

INTRODUCTION

Tuberculosis (TB) is a major health problem worldwide. The BCG, the only authorized vaccine to fight TB, shows a variable protection in the adult population highlighting the need of a new vaccine. Immunoinformatics offers a variety of tools that can predict immunogenic T-cell peptides of Mycobacterium tuberculosis (Mtb) that can be used to create a new vaccine. Immunoinformatics has made possible the identification of immunogenic T-cell peptides of Mtb that have been tested in vitro showing a potential for using these molecules as part of a new TB vaccine.

AREAS COVERED

This review summarizes the most common immunoinformatics tools to identify immunogenic T-cell peptides and presents a compilation about research studies that have identified T-cell peptides of Mtb by using immunoinformatics. Also, it is provided a summary of the TB vaccines undergoing clinical trials.

EXPERT OPINION

In the next few years, the field of peptide-based vaccines will keep growing along with the development of more efficient and sophisticated immunoinformatic tools to identify immunogenic peptides with a greater accuracy.

The Utility of Supertype Clustering in Prediction for Class II MHC-Peptide Binding

MOTIVATION

Extensive efforts have been devoted to understanding the antigenic peptides binding to MHC class I and II molecules since they play a fundamental role in controlling immune responses and due their involvement in vaccination, transplantation, and autoimmunity. The genes coding for the MHC molecules are highly polymorphic, and it is difficult to build computational models for MHC molecules with few know binders. On the other hand, previous studies demonstrated that some MHC molecules share overlapping peptide binding repertoires and attempted to group them into supertypes. Herein, we present a framework of the utility of supertype clustering to gain more information about the data to improve the prediction accuracy of class II MHC-peptide binding.

RESULTS

We developed a new method, called superMHC, for class II MHC-peptide binding prediction, including three MHC isotypes of HLA-DR, HLA-DP, and HLA-DQ, by using supertype clustering in conjunction with RLS regression. The supertypes were identified by using a novel repertoire dissimilarity index to quantify the difference in MHC binding specificities. The superMHC method achieves the state-of-the-art performance and is demonstrated to predict binding affinities to a series of MHC molecules with few binders accurately. These results have implications for understanding receptor-ligand interactions involved in MHC-peptide binding.

Improved methods for predicting peptide binding affinity to MHC class II molecules

Major histocompatibility complex class II (MHC-II) molecules are expressed on the surface of professional antigen-presenting cells where they display peptides to T helper cells, which orchestrate the onset and outcome of many host immune responses. Understanding which peptides will be presented by the MHC-II molecule is therefore important for understanding the activation of T helper cells and can be used to identify T-cell epitopes. We here present updated versions of two MHC-II-peptide binding affinity prediction methods, NetMHCII and NetMHCIIpan. These were constructed using an extended data set of quantitative MHC-peptide binding affinity data obtained from the Immune Epitope Database covering HLA-DR, HLA-DQ, HLA-DP and H-2 mouse molecules. We show that training with this extended data set improved the performance for peptide binding predictions for both methods. Both methods are publicly available at www.cbs.dtu.dk/services/NetMHCII-2.3 and www.cbs.dtu.dk/services/NetMHCIIpan-3.2.

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification

A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major histocompatibility complex class II (MHC class II) molecules. The bound peptide is then presented on the cell surface where it can be recognized by T helper lymphocytes. NetMHCIIpan is a state-of-the-art method for the quantitative prediction of peptide binding to any human or mouse MHC class II molecule of known sequence. In this paper, we describe an updated version of the method with improved peptide binding register identification. Binding register prediction is concerned with determining the minimal core region of nine residues directly in contact with the MHC binding cleft, a crucial piece of information both for the identification and design of CD4(+) T cell antigens. When applied to a set of 51 crystal structures of peptide-MHC complexes with known binding registers, the new method NetMHCIIpan-3.1 significantly outperformed the earlier 3.0 version. We illustrate the impact of accurate binding core identification for the interpretation of T cell cross-reactivity using tetramer double staining with a CMV epitope and its variants mapped to the epitope binding core. NetMHCIIpan is publicly available at http://www.cbs.dtu.dk/services/NetMHCIIpan-3.1 .

Identification of Novel Potential Vaccine Candidates against Tuberculosis Based on Reverse Vaccinology

Tuberculosis (TB) is a chronic infectious disease, considered as the second leading cause of death worldwide, caused by Mycobacterium tuberculosis. The limited efficacy of the bacillus Calmette-Guérin (BCG) vaccine against pulmonary TB and the emergence of multidrug-resistant TB warrants the need for more efficacious vaccines. Reverse vaccinology uses the entire proteome of a pathogen to select the best vaccine antigens by in silico approaches. M. tuberculosis H37Rv proteome was analyzed with NERVE (New Enhanced Reverse Vaccinology Environment) prediction software to identify potential vaccine targets; these 331 proteins were further analyzed with VaxiJen for the determination of their antigenicity value. Only candidates with values ≥0.5 of antigenicity and 50% of adhesin probability and without homology with human proteins or transmembrane regions were selected, resulting in 73 antigens. These proteins were grouped by families in seven groups and analyzed by amino acid sequence alignments, selecting 16 representative proteins. For each candidate, a search of the literature and protein analysis with different bioinformatics tools, as well as a simulation of the immune response, was conducted. Finally, we selected six novel vaccine candidates, EsxL, PE26, PPE65, PE_PGRS49, PBP1, and Erp, from M. tuberculosis that can be used to improve or design new TB vaccines.

Characterization of a cross-reactive, immunodominant and HLA-promiscuous epitope of Mycobacterium tuberculosis-specific major antigenic protein PPE68

PPE68 (Rv3873), a major antignic protein encoded by Mycobacteriun tuberculosis-specific genomic region of difference (RD)1, is a strong stimulator of peripheral blood mononuclear cells (PBMCs) obtained from tuberculosis patients and Mycobacterium bovis bacillus Calmette Guerin (BCG)-vaccianted healthy subjects in T helper (Th)1 cell assays, i.e. antigen-induced proliferation and interferon-gamma (IFN-γ) secretion. To confirm the antigen-specific recognition of PPE68 by T cells in IFN-γ assays, antigen-induced human T-cell lines were established from PBMCs of M. Bovis BCG-vaccinated and HLA-heterogeneous healthy subjects and tested with peptide pools of RD1 proteins. The results showed that PPE68 was recognized by antigen-specific T-cell lines from HLA-heteregeneous subjects. To further identify the immunodominant and HLA-promiscuous Th1-1 cell epitopes present in PPE68, 24 synthetic peptides covering the sequence of PPE68 were indivdually analyzed for HLA-DR binding prediction analysis and tested with PBMCs from M. bovis BCG-vaccinated and HLA-heterogeuous healthy subjects in IFN-γ assays. The results identified the peptide P9, i.e. aa 121-VLTATNFFGINTIPIALTEMDYFIR-145, as an immunodominant and HLA-DR promiscuous peptide of PPE68. Furthermore, by using deletion peptides, the immunodominant and HLA-DR promiscuous core sequence was mapped to aa 127-FFGINTIPIA-136. Interestingly, the core sequence is present in several PPE proteins of M. tuberculosis, and conserved in all sequenced strains/species of M. tuberculosis and M. tuberculosis complex, and several other pathogenic mycobacterial species, including M. leprae and M. avium-intracellulalae complex. These results suggest that the peptide aa 121-145 may be exploited as a peptide-based vaccine candidate against tuberculosis and other mycobacterial diseases.

In silico analysis and experimental validation of Mycobacterium tuberculosis -specific proteins and peptides of Mycobacterium tuberculosis for immunological diagnosis and vaccine development

Comparative analyses of the Mycobacterium tuberculosis genome with the genomes of other mycobacteria have led to the identification of several genomic regions of difference (RDs) between M. tuberculosis and M. bovis BCG. The identification of immunodominant and HLA-promiscuous antigens and peptides encoded by these RDs could be useful for diagnosis and the development of new vaccines against tuberculosis. The analysis of RD proteins and peptides by in silico methods (using computational programs to predict major and HLA-promiscuous antigenic proteins and peptides) and experimental validations (using peripheral blood mononuclear cells and sera from tuberculosis patients and BCG-vaccinated healthy subjects to assess antigen-specific cellular and humoral immune responses in vitro) identified several major antigens and peptides. To evaluate the in vivo potentials, the genes of immunodominant antigens were cloned and expressed in DNA vaccine vectors. Immunizations of experimental animals with the recombinant constructs induced antigen-specific cellular responses. Further experiments showed that each of these proteins had several T and B cell epitopes scattered throughout their sequence, which confirmed their strong immunogenicity. In conclusion, the bioinformatics-based in silico identification of promiscuous antigens and peptides of M. tuberculosis is a useful approach to identify new candidates important for diagnosis and vaccine applications.

Comparative evaluation of MPT83 (Rv2873) for T helper-1 cell reactivity and identification of HLA-promiscuous peptides in Mycobacterium bovis BCG-vaccinated healthy subjects

MPT83 (Rv2873), a surface lipoprotein excreted in the culture of Mycobacterium tuberculosis, is immunoreactive in antibody assays in humans and animals and provides protection as a combined DNA vaccine in mice and cattle. This study was undertaken to determine the reactivity of MPT83 in T helper 1 (Th1)-cell assays, i.e., antigen-induced proliferation and gamma interferon (IFN-γ) secretion, using peripheral blood mononuclear cells (PBMCs) obtained from Mycobacterium bovis bacillus Calmette-Guérin (BCG)-vaccinated and/or M. tuberculosis-infected healthy subjects. PBMCs were tested with complex mycobacterial antigens and pools of synthetic peptides corresponding to MPT63, MPT83, MPB70, LppX, PPE68, CFP10, and ESAT-6. The results showed that MPT83 is among the strongest Th1 cell antigens of M. tuberculosis, and it was recognized equally strongly by BCG-vaccinated and by BCG-vaccinated and M. tuberculosis-infected healthy subjects. Furthermore, HLA heterogeneity of the responding donors suggested that MPT83 was presented to Th1 cells by several HLA-DR molecules. The analysis of the mature MPT83 sequence (amino acids [aa] 1 to 220) and its 14 overlapping synthetic peptides for binding prediction to HLA class II molecules and actual recognition of the peptides by PBMCs from HLA-DR-typed subjects in antigen-induced proliferation and IFN-γ assays suggested that Th1 cell epitopes were scattered throughout the sequence of MPT83. In addition, the HLA-promiscuous nature of at least three peptides, i.e., P11 (aa 151 to 175), P12 (aa 166 to 190), and P14 (aa 196 to 220), was suggested by HLA-DR binding predictions and recognition by HLA-DR heterogeneous donors in Th1 cell assays. These results support the inclusion of MPT83 in an antigen cocktail to develop a new antituberculosis vaccine.

Cytokines in response to proteins predicted in genomic regions of difference of Mycobacterium tuberculosis

Cellular immune responses are responsible for both protection and pathogenesis in tuberculosis, and are mediated/regulated by a complex network of pro-inflammatory, T helper (Th) type 1 and type 2 cytokines. In this study, the secretion of pro-inflammatory cytokines tumor necrosis factor-alpha (TNF-α), interleukin (IL)-6, IL-8 and IL-1β; Th1 cytokines interferon-gamma (IFN-γ), IL-2 and tumor necrosis factor-beta (TNF-β); and Th2 cytokines IL-4, IL-5 and IL-10 by the peripheral blood mononuclear cells (PBMCs) of pulmonary tuberculosis patients was studied. PBMCs were cultured in vitro in the absence and presence of complex mycobacterial antigens and peptides corresponding to 11 regions of difference (RD) of Mycobacterium tuberculosis that are deleted/absent in all vaccine strains of Mycobacterium bovis bacillus Calmette-Guérin (BCG). The culture supernatants were tested for secreted cytokines by FlowCytomix assay. PBMCs from the majority of patients (53-100%) spontaneously secreted detectable concentrations of all cytokines tested, except for IL2 (29%) and IL-10 (41%). The profiles of proinflammatory cytokines were largely similar for various complex antigens or RD peptides. However, with respect to Th1 and Th2 cytokines, the antigens could be divided into three groups; the first with Th1-bias (culture filtrate of M. tuberculosis, RD1, RD5, RD7, RD9 and RD10), the second with Th2-bias (whole cells and cell walls of M. tuberculosis, RD12, RD13 and RD15), and the third without Th1/Th2-bias (M. bovis BCG, RD4, RD6 and RD11). Complex mycobacterial antigens and RD proteins with Th1- and Th2-biases may have roles in protection and pathogenesis of tuberculosis, respectively.

Identification of HLA-DR4-restricted T-cell epitope on MPT51 protein, a major secreted protein derived from Mycobacterium tuberculosis using MPT51 overlapping peptides screening and DNA vaccination

We identified a novel HLA-DR4-restricted CD4+ T-cell epitope on a secreted antigen of Mycobacterium tuberculosis, MPT51, in 004149-MM HLA-DR4-transgenic mice which express HLA-DRB1*0401, but not murine MHC class II molecules. The mice were immunized with plasmid DNA encoding MPT51 using gene gun and interferon (IFN)-gamma production from the immune splenocytes was analyzed. In response to overlapping synthetic peptides covering the mature MPT51 sequence, only one peptide, p191-210, stimulated the splenocytes to produce IFN-gamma. Further analysis using flow cytometry and computer-assisted algorithm, ProPred, narrowed down the region of CD4+ T-cell epitope to p191-202. The CD4+ T-cell epitope would be feasible for vaccine design against tuberculosis as well as for analysis of MPT51-specific T-cells in M. tuberculosis infection.

MHC class II epitope predictive algorithms

SUMMARY

Major histocompatibility complex class II (MHC-II) molecules sample peptides from the extracellular space, allowing the immune system to detect the presence of foreign microbes from this compartment. To be able to predict the immune response to given pathogens, a number of methods have been developed to predict peptide-MHC binding. However, few methods other than the pioneering TEPITOPE/ProPred method have been developed for MHC-II. Despite recent progress in method development, the predictive performance for MHC-II remains significantly lower than what can be obtained for MHC-I. One reason for this is that the MHC-II molecule is open at both ends allowing binding of peptides extending out of the groove. The binding core of MHC-II-bound peptides is therefore not known a priori and the binding motif is hence not readily discernible. Recent progress has been obtained by including the flanking residues in the predictions. All attempts to make ab initio predictions based on protein structure have failed to reach predictive performances similar to those that can be obtained by data-driven methods. Thousands of different MHC-II alleles exist in humans. Recently developed pan-specific methods have been able to make reasonably accurate predictions for alleles that were not included in the training data. These methods can be used to define supertypes (clusters) of MHC-II alleles where alleles within each supertype have similar binding specificities. Furthermore, the pan-specific methods have been used to make a graphical atlas such as the MHCMotifviewer, which allows for visual comparison of specificities of different alleles.

Immunoproteomic identification of human T cell antigens of Mycobacterium tuberculosis that differentiate healthy contacts from tuberculosis patients

Identification of Mycobacterium tuberculosis antigens inducing cellular immune responses is required to improve the diagnosis of and vaccine development against tuberculosis. To identify the antigens of M. tuberculosis that differentiated between tuberculosis (TB) patients and healthy contacts based on T cell reactivity, the culture filtrate of in vitro grown M. tuberculosis was fractionated by two-dimensional liquid phase electrophoresis and tested for the ability to stimulate T cells in a whole blood assay. This approach separated the culture filtrate into 350 fractions with sufficient protein quantity (at least 200 microg of protein) for mass spectrometry and immunological analyses. High levels of interferon-gamma (IFN-gamma) secretion were induced by 105 fractions in healthy contacts compared with TB patients (p < 0.05). Most interesting was the identification of 10 fractions that specifically induced strong IFN-gamma production in the healthy contact population but not in TB patients. Other immunological measurements showed 42 fractions that induced significant lymphocyte proliferative responses in the healthy contact group compared with the TB patients. The tumor necrosis factor-alpha response for most of the fractions did not significantly differ in the tested groups, and the interleukin-4 response was below the detectable range for all fractions and both study groups. Proteomic characterization of the 105 fractions that induced a significant IFN-gamma response in the healthy contacts compared with the TB patients led to the identification of 59 proteins of which 24 represented potentially novel T cell antigens. Likewise, the protein identification in the 10 healthy "contact-specific fractions" revealed 16 proteins that are key candidates as vaccine or diagnostic targets.

Characterization of human cellular immune responses to novel Mycobacterium tuberculosis antigens encoded by genomic regions absent in Mycobacterium bovis BCG

Comparative genomics has identified several regions of differences (RDs) between the infectious Mycobacterium tuberculosis and the vaccine strains of Mycobacterium bovis BCG. We aimed to evaluate the cellular immune responses induced by antigens encoded by genes predicted in 11 RDs. Synthetic peptides covering the sequences of RD1, RD4 to RD7, RD9 to RD13, and RD15 were tested for antigen-induced proliferation and secretion of Th1 cytokine, gamma interferon (IFN-gamma), by peripheral blood mononuclear cells (PBMC) obtained from culture-proven pulmonary tuberculosis (TB) patients and M. bovis BCG-vaccinated healthy subjects. Among the peptide pools, RD1 induced the best responses in both donor groups and in both assays. In addition, testing of TB patients' PBMC for secretion of proinflammatory cytokines (tumor necrosis factor alpha [TNF-alpha], interleukin 6 [IL-6], IL-8, and IL-1beta), Th1 cytokines (IFN-gamma, IL-2, and TNF-beta), and Th2 cytokines (IL-4, IL-5, and IL-10) showed differential effects of RD peptides in the secretion of IFN-gamma and IL-10, with high IFN-gamma/IL-10 ratios (32 to 5.0) in response to RD1, RD5, RD7, RD9, and RD10 and low IFN-gamma/IL-10 ratios (<1.0) in response to RD12, RD13, and RD15. Peptide-mixing experiments with PBMC from healthy subjects showed that secretion of large quantities of IL-10 in response to RD12 and RD13 correlated with inhibition of Th1 responses induced by RD1 peptides. In conclusion, our results suggest that M. tuberculosis RDs can be divided into two major groups--one group that activates PBMC to preferentially secrete IFN-gamma and another group that activates preferential secretion of IL-10--and that these two groups of RDs may have roles in protection against and pathogenesis of TB, respectively.

Efficient testing of large pools of Mycobacterium tuberculosis RD1 peptides and identification of major antigens and immunodominant peptides recognized by human Th1 cells

Comparative genomics has identified several regions of difference (RDs) of Mycobacterium tuberculosis that are deleted or absent in Mycobacterium bovis BCG vaccines. To determine their relevance for diagnostic and vaccine applications, it is imperative that efficient methods are developed to test the encoded proteins for immunological reactivity. In this study, we have used 220 synthetic peptides covering sequences of 12 open reading frames (ORFs) of RD1 and tested them as a single pool (RD1(pool)) with peripheral blood mononuclear cells obtained from pulmonary tuberculosis (TB) patients and M. bovis BCG-vaccinated healthy subjects in Th1 cell assays that measure antigen-induced proliferation and IFN-gamma secretion. The results showed that RD1(pool) induced strong responses in both TB patients and BCG-vaccinated healthy subjects. The subsequent testing of peptide pools of individual ORFs revealed that all ORFs induced positive responses in a portion of donors, but PPE68, CFP10, and ESAT6 induced strong responses in TB patients and PPE68 induced strong responses in BCG-vaccinated healthy subjects. In addition, HLA-DR and -DQ typing of donors and HLA-DR binding prediction analysis of proteins suggested HLA-promiscuous presentation of PPE68, CFP10, and ESAT6. Further testing of individual peptides showed that a single peptide of PPE68 (121-VLTATNFFGINTIPIALTEMDYFIR-145) was immunodominant. The search for sequence homology revealed that a part of this peptide, 124-ATNFFGINTIPIAL-137, was present in several PPE family proteins of M. tuberculosis and M. bovis BCG vaccines. Further experiments limited the promiscuous and immunodominant epitope region to the 10-amino-acid cross-reactive sequence 127-FFGINTIPIA-136.

Whole blood assays to identify Th1 cell antigens and peptides encoded by Mycobacterium tuberculosis-specific RD1 genes

OBJECTIVE

To identify Th1 cell-stimulating antigens/peptides encoded by the genes predicted in the Mycobacterium tuberculosis-specific genomic region of difference (RD)1, deleted in Mycobacterium bovis Bacille Calmette-Guérin(BCG), by using synthetic peptides and whole blood from tuberculosis (TB) patients.

MATERIALS AND METHODS

Heparinized peripheral blood was obtained from culture-proven pulmonary TB patients (n = 16) attending the Chest Disease Hospital, Kuwait. Whole blood was diluted with tissue culture medium RPMI-1640 and tested for Th1 cell stimulation using antigen-induced proliferation and interferon-gamma (IFN-gamma) secretion assays. The antigens included a peptide pool of 220 peptides covering the sequence of 12 open reading frames (ORFs) of RD1 (RD1(mix)), peptide pools of RD1 ORF5 (ORF5(mix)), ORF6 (ORF6(mix)) and ORF7 (ORF7(mix)), and individual peptides of ORF6 (P6.1-P6.6) and ORF7 (P7.1-P7.6). M. tuberculosis culture filtrate, cell walls and whole-cell M. bovis BCG were used as complex mycobacterial antigens. The results obtained with different antigens and peptides were statistically analyzed for significant differences using Z test.

RESULTS

The complex mycobacterial antigens (culture filtrate, cell walls and M.bovis BCG) and RD1(mix) induced comparable (p > 0.05) positive antigen-induced proliferation and IFN-gamma responses with whole blood from TB patients. However, the positive IFN-gamma responses induced by ORF6(mix) and ORF7(mix) were higher than ORF5(mix). Among the individual peptides, P6.4 and P7.1 of ORF6 and ORF7, respectively, induced the highest IFN-gamma responses, suggesting that these peptides represented the immunodominant Th1 cell epitopes of RD1 ORF6 and ORF7 in the patients tested.

CONCLUSION

The whole blood assays with synthetic peptides are useful to identify Th1 cell antigens/peptides encoded by genes located in M. tuberculosis-specific genomic regions.

Immunoinformatics: an overview of computational tools and techniques for understanding immune function

In recent years, there has been a rapid expansion in the application of information technology to biological data. Although the use of information science techniques is less common for the discipline of immunology, this field has seen great strides in recent years. This review addresses why in silico modeling is needed in immunology research, highlights some of the major areas of research and suggests what may be important for the future of immunoinformatics.

Direct ex vivo analyses of HLA-DR1 transgenic mice reveal an exceptionally broad pattern of immunodominance in the primary HLA-DR1-restricted CD4 T-cell response to influenza virus hemagglutinin

The recent threat of an avian influenza pandemic has generated significant interest in enhancing our understanding of the events that dictate protective immunity to influenza and in generating vaccines that can induce heterosubtypic immunity. Although antigen-specific CD4 T cells are known to play a key role in protective immunity to influenza through the provision of help to B cells and CD8 T cells, little is known about the specificity and diversity of CD4 T cells elicited after infection, particularly those elicited in humans. In this study, we used HLA-DR transgenic mice to directly and comprehensively identify the specificities of hemagglutinin (HA)-specific CD4 T cells restricted to a human class II molecule that were elicited following intranasal infection with a strain of influenza virus that has been endemic in U.S. human populations for the last decade. Our results reveal a surprising degree of diversity among influenza virus-specific CD4 T cells. As many as 30 different peptides, spanning the entire HA protein, were recognized by CD4 T cells, including epitopes genetically conserved among H1, H2, and H5 influenza A viruses. We also compared three widely used major histocompatibility class II algorithms to predict HLA-DR binding peptides and found these as yet inadequate for identifying influenza virus-derived epitopes. The results of these studies offer key insights into the spectrum of peptides recognized by HLA-DR-restricted CD4 T cells that may be the focus of immune responses to infection or to experimental or clinical vaccines in humans.

LppX is a lipoprotein required for the translocation of phthiocerol dimycocerosates to the surface of Mycobacterium tuberculosis

Cell envelope lipids play an important role in the pathogenicity of mycobacteria, but the mechanisms by which they are transported to the outer membrane of these prokaryotes are largely unknown. Here, we provide evidence that LppX is a lipoprotein required for the translocation of complex lipids, the phthiocerol dimycocerosates (DIM), to the outer membrane of Mycobacterium tuberculosis. Abolition of DIM transport following disruption of the lppX gene is accompanied by an important attenuation of the virulence of the tubercle bacillus. The crystal structure of LppX unveils an U-shaped beta-half-barrel dominated by a large hydrophobic cavity suitable to accommodate a single DIM molecule. LppX shares a similar fold with the periplasmic molecular chaperone LolA and the outer membrane lipoprotein LolB, which are involved in the localization of lipoproteins to the outer membrane of Gram-negative bacteria. Based on the structure and although an indirect participation of LppX in DIM transport cannot yet be ruled out, we propose LppX to be the first characterized member of a family of structurally related lipoproteins that carry lipophilic molecules across the mycobacterial cell envelope.

Recombinant and synthetic peptides to identify Mycobacterium tuberculosis antigens and epitopes of diagnostic and vaccine relevance

The failures of Bacillus Calmette Guerin (BCG) as a vaccine and purified protein derivative as a diagnostic reagent in controlling the worldwide prevalence of tuberculosis (TB) have accelerated the research to identify Mycobacterium tuberculosis-specific antigens that could be useful as new vaccines and diagnostic reagents against TB. In the recent years, the comparative analyses of M. tuberculosis genome with the genomes of other mycobacteria have led to the identification of several genomic regions of M. tuberculosis that are deleted in BCG and other mycobacteria. These deleted regions (RDs) are predicted to encode over 100 proteins. If found immunologically reactive, the proteins encoded by M. tuberculosis-specific RDs could be useful in the specific diagnosis of TB and developing new vaccines. Among the approaches available for immunological characterization of the predicted M. tuberculosis-specific proteins are the evaluations of recombinant proteins and/or overlapping synthetic peptides, covering the sequence of each protein, for antibody and/or Th1 cell reactivity. These approaches have resulted into the identification of several antigenic proteins of M. tuberculosis encoded by genes located in RD1 with potentials in specific diagnosis of TB in low endemic areas and/or development of new vaccines, e.g. ORF14, ESAT6, CFP10, PE, PPE proteins, etc. In addition, prediction programs to identify peptides that could bind several HLA molecules, and presented to T-cells in a promiscuous manner, have been developed. These programs have been used, on a limited scale, to identify the promiscuous peptides encoded by the genes spanning the M. tuberculosis-specific sequence. The promiscuous antigens/peptides recognized by T-cells in cell mediated immunity assays may have potentials in developing peptide-based vaccines and diagnostic reagents against TB.

ProPred analysis and experimental evaluation of promiscuous T-cell epitopes of three major secreted antigens of Mycobacterium tuberculosis

In the search for safe vaccine candidates against tuberculosis (TB), subunit vaccines including peptide-based candidates deserve consideration. However, an important requirement for such vaccine candidates is their promiscuous presentation to Th1 cells mediating protective immunity against TB, i.e. Th1 cells secreting IFN-gamma. The aim of the present study was to identify promiscuous Th1 cell epitopes of three major secreted antigens of Mycobacterium tuberculosis, i.e. ESAT-6, CFP10 and MPT70 by using a virtual matrix-based prediction program (ProPred) for peptide binding to 51 HLA-DR alleles. The ProPred analysis of these proteins was performed using the server (http:www.imtech.res.in/raghava/ProPed/). The peptides predicted to bind > 50% HLA-DR alleles included in the ProPred were considered promiscuous for binding predictions. Based on this criteria, one region in ESAT-6 (aa 69-77), two regions in CFP10 (aa 55-66 and aa 76-84) and four regions in MPT70 (aa 1-11, aa 81-95, aa 124-140 and aa 182-191) were considered promiscuous HLA-DR binders. The experimental evaluation of these regions, by using overlapping synthetic peptides for presentation to T-cells, confirmed the promiscuous nature of peptides covering the regions aa 69-77, aa 76-84 and aa 182-191 of ESAT-6, CFP10 and MPT70, respectively. These results demonstrate that the ProPred analysis can facilitate the selection of promiscuous peptides recognized by Th1 cells, and thus it can be useful in the identification of peptide-based vaccine candidates against TB.

Chimeric epitopes delivered by polymeric synthetic linear peptides induce protective immunity to malaria

Polymeric linear peptide chimeras (LPCs) that incorporate Plasmodium vivax promiscuous T cell epitopes and the P. falciparum circumsporozoite protein B cell epitope have been shown to induce a high level of immunogenicity and overcome genetic restriction when tested as vaccine immunogens in BALB/c mice. The present study evaluates the biological relevance of several LPCs using a well characterized rodent malaria model. Polymeric peptide constructs based on P. berghei and P. yoelii sequences, and orthologous to the human malaria sequences included in the original LPCs, were designed and tested for immunogenicity in mice of different H-2 haplotypes. We demonstrate that robust immune responses are induced and that peptides containing the orthologous rodent Plasmodium sequences exhibited similar immunogenic capabilities. Unique to this report, we show that LPCs can also prime MHC class I-restricted cytotoxic T lymphocytes (CTLs) and, most relevantly, that a peptide construct prototype incorporating single B, T and CTL epitopes induced protection against an experimental challenge with P. berghei or P. yoelii sporozoites. Collectively, these results suggest that polymeric polypeptide chimeras can be used as a platform to deliver subunit vaccines.

HLA-DR binding prediction and experimental evaluation of T-cell epitopes of mycolyl transferase 85B (Ag85B), a major secreted antigen of Mycobacterium tuberculosis

OBJECTIVE

To identify T-cell epitopes of Ag85B by analysis of its sequence for prediction to bind HLA-DR alleles and evaluate the predicted peptides for recognition by T cells in antigen-induced proliferation assays.

MATERIALS/SUBJECTS AND METHODS

The complete sequence of Ag85B was analyzed for HLA-DR binding prediction to 51 HLA-DR alleles by using a virtual matrix-based prediction program (ProPred). Synthetic peptides covering the sequence of mature Ag85B were also analyzed for binding to HLA-DR alleles, and evaluated for recognition in antigen-induced proliferation assays with Ag85B-specific T-cell lines established from the peripheral blood mononuclear cells of 10 HLA-DR-heterogeneous tuberculosis patients.

RESULTS

The ProPred analysis of the full-length Ag85B (325 aa), signal peptide (40 aa) and the mature protein (285 aa) predicted their binding to 100, 76 and 98% of the 51 HLA-DR alleles, respectively. The analysis of 31 synthetic peptides for binding to HLA-DR alleles showed that 4 of them could bind >50% HLA-DR alleles, and were considered promiscuous. Testing of Ag85B-specific T-cell lines with synthetic peptides showed that all of the T-cell lines responded to one or more peptides of Ag85B, and 9 of the 10 cell lines responded to one or more of the four peptides considered promiscuous for binding to HLA-DR alleles.

CONCLUSION

The ProPred program was useful in predicting the HLA-DR alleles binding regions of Ag85B and identifying the promiscuous peptides recognized by T cells.

TB subunit vaccines—putting the pieces together

The search for a new and improved vaccine against tuberculosis (TB) is currently a very active field of research, which in the last 10 years has benefited tremendously from the completed Mycobacterium tuberculosis genome and the progress in molecular biology and computer science. In this review, we discuss how Genomics, Proteomics and Transcriptomics have accelerated the pace of antigen discovery and vaccine development and have changed this field completely, resulting in the identification of a large number of antigens with potential in TB vaccines. The next phase of this work has now started--putting the most relevant molecules back together as fusion molecules and cocktails. This requires carefully monitoring aspects as immunodominance, recognition in different populations as well as vaccine manufacturing.

Mycobacterial gene cloning and expression, comparative genomics, bioinformatics and proteomics in relation to the development of new vaccines and diagnostic reagents

Recent advances in molecular and genomic techniques have facilitated research on several aspects of mycobacteriology, such as diagnosis and the identification of new vaccines and therapeutic targets for various diseases, including tuberculosis. The aim of this review was to analyze the implications of advances in molecular and genomic techniques on the development of new vaccines for tuberculosis as well as immunological reagents to diagnose the disease. Gene cloning and expression, DNA and protein sequencing, polymerase chain reaction, comparative genomics, bioinformatics, proteomics and DNA and peptide synthesis coupled with the application of cellular immunology techniques have led to the identification of several antigens of Mycobacterium tuberculosis, which have potential for diagnosis and vaccine applications. For example, cross-reactive mycobacterial antigens like heat shock proteins, MTB32 and MTB39, have been identified as new vaccine candidates, and antigens encoded by M. tuberculosis-specific genomic regions as new reagents for diagnosis.

In vitro cellular immune responses to complex and newly defined recombinant antigens of Mycobacterium tuberculosis

The immunological diagnosis and development of new antituberculosis vaccines require the characterization of Mycobacterium tuberculosis antigens inducing cell-mediated immune responses. In this study, we have tested peripheral blood mononuclear cells (PBMC) from tuberculosis (TB) patients (n = 43) and Bacille Calmette-Guérin (BCG)-vaccinated healthy subjects (n = 24) for in vitro cellular immune responses, as indicated by antigen-induced proliferation and interferon (IFN)-gamma secretion, in response to a panel of complex (culture filtrate and cell wall preparations) and single recombinant antigens (Mtb8.4, Mtb9.8, Mtb9.9, Mtb32A, Mtb39A, Mtb40, Mtb41 and Ag85B) of M. tuberculosis. The results of cellular responses showed that the majority (ranging from 70 to 98%) of TB patients and healthy donors responded to the complex antigens in antigen-induced proliferation and IFN-gamma secretion assays. However, when PBMC from the same groups of patients and healthy donors were tested with the recombinant antigens, TB patients showed strong recognition (>50% responders) of Mtb9.8 and Mtb39A in proliferation assays (median SI = 6.2 and 6.4, respectively) and of Mtb9.8, Mtb39A, Mtb40 and Ag85B in IFN-gamma assays (median delta IFN-gamma= 15.5, 10.8, 7.8 and 8.1 U/ml, respectively). BCG-vaccinated healthy donors showed weak (<30% responders) to moderate (31-50% responders) responses to all of the recombinant antigens in both assays. When PBMC of a subset of TB patients (n = 11) were tested for secretion of protective Th1 cytokines [IFN-gamma, tumour necrosis factor (TNF)-alpha and interleukin (IL)-12] and the immunosuppressive cytokine IL-10, the complex CF and CW antigens as well as the recombinant Mtb9.8, Mtb9.9, Mtb40 and Ag85B induced the secretion of both types of cytokines. On the other hand, Mtb41 induced only IL-10, while Mtb8.4, Mtb32Aand Mtb39A induced the secretion of one or more of Th1 cytokines, but not IL-10. In conclusion, the recombinant antigens inducing the secretion of Th1 cytokines could be useful as subunit vaccine candidates against TB.