Analysis of predicted CD8+ T cell epitopes from proteins encoded by the specific RD regions of Mycobacterium tuberculosis for vaccine development and specific diagnosis

Prediction of a novel synthetic peptide vaccine against tuberculosis and validation of its immunogenicity

BACKGROUND

Tuberculosis (TB) is an infectious disease transmitted through the respiratory system that affects people worldwide. Bacillus Calmette-Guérin (BCG), the only approved TB vaccine, has been shown to have highly variable protective efficacy in different populations and is ineffective at protecting adults. Therefore, the development of more effective TB vaccines is vital.

METHODS

Three dominant antigens (ESAT6, CFP10, and MPT64) from the region of difference were selected for this study. Their physicochemical properties, spatial structures, and immune responses were evaluated using bioinformatics screening of dominant T cell and B cell epitopes. Three vaccine constructs were developed. After selecting the appropriate linkers, their physicochemical properties, spatial structures, and immune responses of the vaccines were evaluated, and molecular dynamics simulations were performed to test their ability to bind to major histocompatibility complex (MHC) receptors within 100 ns. This process aimed to create highly antigenic vaccine constructs capable of eliciting an immune response. The effects of the vaccine constructs on the host immune response were assessed using enzyme-linked immunosorbent assays, flow cytometry, and hematoxylin and eosin staining.

RESULTS

A novel peptide vaccine, designated ECM-64, was developed by screening six immunodominant peptides from three antigens and constructing independent T-epitope and B-epitope vaccines. Compared weith BCG-immunized mice, ECM-64-immunized mice exhibited a substantial augmentation in Th1/Th2 cytokine secretion and CD3+CD4+T and CD3+CD8-T lymphocyte counts. ECM-64-specific IgG and IgG1 antibodies were produced after immunization. The immunoinformatics findings were largely consistent with those obtained from the analysis of immunized mice.

CONCLUSION

ECM-64 is a promising multipeptide TB vaccine with the advantage of inducing high levels of Th1/Th2 cytokines, antibodies, and CD3+CD4+T and CD3+CD8-T lymphocytes in mice. This study also provides preliminary evidence that bioinformatic methods can be used to screen for dominant epitopes. These findings lay the groundwork for the development of peptide-based TB vaccines.

Role of ESAT-6 in pathogenicity of Beijing and non-Beijing Mycobacterium tuberculosis isolates

BACKGROUND

Mycobacterium tuberculosis Beijing genotype was associated with tuberculosis outbreaks and increased transmissibility. To understand the variation in virulence between Beijing and non-Beijing clinical isolates of M.tuberculosis genotypes, the esat-6 gene sequencing, and its expression was compared in the macrophage environment.

MATERIALS & METHODS

Among 64 nonrepetitive, culture-positive M.tuberculosis, DNA extraction of 24 and 40 pure confirmed Beijing and non-Beijing isolates was accompanied by the boiling method. esat-6 gene PCR amplification and their sequencing were carried out by specific primers and its expression was performed on human macrophage cell line U937 after 6, 12, and 18 h of exposure to bacilli. The esat-6 mRNA transcription and expression in M. tuberculosis treated macrophage by Real-Time PCR and Western blot method.

RESULTS

Data analysis based on sequencing of the east-6 gene PCR product showed that this gene exists in all isolates and there are no changes or single nucleotide variation between the Beijing and non-Beijing isolates. In Beijing strains, the esat-6 expression was increased during the study times, but it was constant in non-Beijing isolates. esat-6 gene expression in Beijing isolates reached to about 44.9 times more than non-Beijing isolates after 18 h incubation on the macrophages cell line.

CONCLUSION

esat-6 is a conserved gene both in Beijing and non-Beijing isolates of M.tuberculosis. More expression of the east-6 gene in the macrophage model may indicate that this gene is likely to play a more important role in increasing the pathogenicity of Beijing strains.

Recent progress in the design of DNA vaccines against tuberculosis

Current tuberculosis (TB) vaccines have some disadvantages and many efforts have been undertaken to produce effective TB vaccines. As a result of their advantages, DNA vaccines are promising future vaccine candidates. This review focuses on the design and delivery of novel DNA-based vaccines against TB.

Antigens Rv0310c and Rv1255c are promising novel biomarkers for the diagnosis of Mycobacterium tuberculosis infection

This study aimed to identify novel immunogenic epitopes from Mycobacterium tuberculosis (MTB) that could be used in tuberculosis (TB) diagnostics. To determine the diagnostic potential of mycobacterial antigens in serodiagnosis of TB, 256 patients were enrolled in a study and divided into two groups: 126 smear-positive pulmonary TB patients (SPPT) and 130 smear-negative pulmonary TB patients (SNPT); 152 bacillus Calmette-Guerin (BCG)-vaccinated healthy people were used as a control. Murine results showed that antigens Rv0310c-E from RD 8 and Rv1255c-E from RD 10 were strongly immunogenic to Th1 cells and induced a great humoral response. Receiver operating characteristic analysis indicated that Rv0310c-E (area under the curve (AUC): 0.800) and Rv1255c-E (AUC: 0.808) performed better than ESAT-6 (AUC: 0.665) and CFP-10 (AUC: 0.623) proteins but were comparable with Rv3425 (AUC: 0.788) protein in a human serum IgG analysis. Rv0310c-E demonstrated the highest diagnostic ability for the SPPT group (Youden index: 0.5602, sensitivity: 69.84%, specificity: 86.18%), while Rv1255c-E demonstrated the highest diagnostic ability for the SNPT group (Youden index: 0.5674, sensitivity: 73.84%, specificity: 82.89%). In addition, combination analysis found that antigen Rv0310c-E, coupled with the Rv3425 protein (Youden index: 0.6098, sensitivity: 87.30%, specificity: 73.68%) had the strongest performance for TB diagnostics of the SPPT group, and the single antigen Rv1255c-E was strongest for the SNPT group. These results suggest that antigens Rv0310c-E and Rv1255c-E are potential antigens for TB serodiagnostic tests, which may facilitate detection of MTB in smear-negative and smear-positive patients.

A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis

Development of an effective vaccine against drug-resistant Mycobacterium tuberculosis (Mtb) is crucial for saving millions of premature deaths every year due to tuberculosis. This paper describes a web portal developed for assisting researchers in designing vaccines against emerging Mtb strains using traditional and modern approaches. Firstly, we annotated 59 genomes of Mycobacterium species to understand similarity/dissimilarity between tuberculoid, non-tuberculoid and vaccine strains at genome level. Secondly, antigen-based vaccine candidates have been predicted in each Mtb strain. Thirdly, epitopes-based vaccine candidates were predicted/discovered in above antigen-based vaccine candidates that can stimulate all arms of immune system. Finally, a database of predicted vaccine candidates at epitopes as well at antigen level has been developed for above strains. In order to design vaccine against a newly sequenced genome of Mtb strain, server integrates three modules for identification of strain-, antigen-, epitope-specific vaccine candidates. We observed that 103522 unique peptides (9mers) had the potential to induce an antibody response and/or promiscuous binder to MHC alleles and/or have the capability to stimulate T lymphocytes. In summary, this web-portal will be useful for researchers working on designing vaccines against Mtb including drug-resistant strains. Availability: The database is available freely at http://crdd.osdd.net/raghava/mtbveb/.

Mycobacterium tuberculosis pellicles express unique proteins recognized by the host humoral response

Mycobacterium tuberculosis (MTB) causes both acute and chronic infections in humans characterized by tolerance to antibiotics and reactivation to cause secondary tuberculosis. These characteristics have led to renewed interest in the in vitro pellicle, or biofilm mode of growth, where bacteria grow to produce a thick aggregate at the air-liquid interface and exhibit increased phenotypic resistance to antibiotics. We infected guinea pigs with the virulent H37Rv strain of MTB for 60 days at which point we collected blood. To identify antigenic proteins, membrane protein extracts of MTB H37Ra pellicles and shaken cultures grown for 3, 5, or 7 weeks were probed with the infected animals' sera after the proteins were separated by two-dimensional gel electrophoresis (2DGE). Antigenic proteins were then identified using MALDI-TOF/TOF mass spectrometry peptide mass fingerprinting. Antigenic pellicle proteins were compared across the three timepoints to identify those that were produced consistently during pellicle growth. They were also compared to those membrane proteins identified from harvested shaken cultures to determine pellicle-specific vs. universally expressed proteins. Using this technique, we identified 44 distinct antigenic proteins, nine of which were pellicle-specific. The sequence of antigenic pellicle-specific proteins was checked for sequence conservation across 15 sequenced MTB clinical isolates, three other members of the MTB complex, as well as M. avium and M. smegmatis. The antigenic pellicle-specific protein Rv0097 was found to have very high sequence conservation within the MTB complex but not with related mycobacteria, while FabG4 was highly conserved in all mycobacteria analyzed. These conserved pellicle-specific proteins represent targets for the development of future diagnostic tests and vaccines.

Antigen-specific CD4- and CD8-positive signatures in different phases of Mycobacterium tuberculosis infection

Current diagnostic standards for Mycobacterium tuberculosis (MTB) infection do not distinguish between active and latent tuberculosis (TB). To identify specific biomarkers characterizing the different forms of TB infection, we investigated in parallel with the QuantiFERON -TB Gold In-Tube (QFT-IT) the use of flow cytometry measuring CD4 and CD8 MTB-specific immune response in 17 active-TB patients, 21 health care workers (HCW), 14 recent contacts of TB patients (RC-TB), and 10 bacille Calmette Guerin (BCG)-vaccinated healthy controls (BCG-HC). A correlation (r = 0.4526, P = 0.0002) was found only between the amount of IFN-γ measured by QFT-IT and the frequency of CD4+/CD69+/IFN-γ+ T cells. The frequency of CD4+/CD69+/IFNγ+ responding T cells was higher in active-TB patients (0.254 ± 0.336%, P < 0.01) compared to the other groups. The response of QFT-IT antigen-specific CD8+/CD69+/IFNγ+ T cells was significantly higher in RC-TB (0.245 ± 0.305%, P < 0.05) compared to the other study groups.

Weak binder for MHC molecule is a potent Mycobacterium tuberculosis-specific CTL epitope in the context of HLA-A24 allele

Tuberculosis causes serious health problem for the world population. Antigenic peptides selected by pathogen-specific cytotoxic T lymphocytes (CTLs) are presented by major histocompatibility complex (MHC; or human leukocyte antigen [HLA] in humans) molecules, and HLA-A restricted responses may be of interest for vaccine development and the understanding of cellular immunity. A series of peptides derived from the 10-KDa culture filtrate protein (CFP10) and the 6 kDa early secretory antigenic target (ESAT-6) in the Mycobacterium tuberculosis (Mtb) have been screened and a CTL epitope restricted by the human leukocyte antigen HLA-A24, a common HLA allele in Asian people, has been identified. In this study, we studied a panel of CFP10 and ESAT-6-derived peptides to identify those with binding motifs for HLA-A24 molecules. The antigenicity of candidate peptides was assessed with in vitro refolding tests and an enzyme-linked immunospot (ELISPOT) assay, and by tetramer staining to determine the capacity to stimulate CTLs from peripheral blood mononuclear cells (PBMCs) of HLA-A24-positive TB Patients. We report that one novel candidate peptide at positions 5-14 of ESAT-6 of Mtb could induce peptide-specific CTLs from PBMCs of HLA-A24-positive patients, but not from HLA-A24-negative patients and HLA-A24-positive healthy controls. Identified epitope is a weak binder for HLA-A24 molecule in a mini MHC refolding assay. Since the peptide is presented by a common HLA class I molecule, it may be useful for immunotherapy against Mtb infection and vaccine development in the large population of Mtb-infected patients.

Tuberculosis vaccine research in China

It is now privately acknowledged that there may be little if any perceptible impact of the national Bacille Calmette-Guerin (BCG) vaccination program on disease prevalence, despite the extensive coverage of the newborn infant population and likely benefit in the early years of life. A better preventive vaccine than BCG is now being sought by Chinese researchers. Urgency has been added to the control problem by the emergence of multidrug-resistant tuberculosis (TB). Furthermore, expensive second-line drugs seem unlikely to be made available by the government to treat drug-resistant cases, so attention in addition has turned to the potential of immunotherapy as an adjunct to chemotherapy. Research trends are summarized here.

In silico identification of potential antigenic proteins and promiscuous CTL epitopes in Mycobacterium tuberculosis

Cell-mediated immunity is critical for the control of Mycobacterium tuberculosis infection. We hypothesized that those proteins of M. tuberculosis (MTB) that do not have homologs in humans as well as human gut flora, would mount a good antigenic response in man, and employed a bioinformatics approach to identify MTB antigens capable of inducing a robust cell-mediated immune response in humans. In the first step we identified 624 MTB proteins that had no homologs in humans. Comparison of this set of proteins with the proteome of 77 different microbes that comprise the human gut flora narrowed down the list to 180 proteins unique to MTB. Twenty nine of the 180 proteins are known to be associated with dormancy. Since dormancy associated proteins are known to harbor CTL epitopes, we selected four representative unique proteins and subjected them to epitope analysis using ProPred1. Nineteen novel promiscuous epitopes were identified in the four proteins. Population coverage for 7 of the 19 shortlisted epitopes including Rv3852 (58-KPAEAPVSL, 112-VPLIVAVTL, 118-VTLSLLALL and 123-LALLLIRQL), Rv2706c (66-RPLSGVSFL) Rv3466 (8- RIVEVFDAL and 38-RSLERLECL) was >74%. These novel promiscuous epitopes are conserved in other virulent MTB strains, and can therefore be further investigated for their immunological relevance and usefulness as vaccine candidates.

TCR mispairing in genetically modified T cells was detected by fluorescence resonance energy transfer

Adoptive transfer of T lymphocytes genetically modified with antigen-specific T cell receptor (TCR) constitutes a promising approach for the treatment of malignant tumors and virus infections. One of the challenges in this field of TCR gene therapy is TCR mispairing defining the incorrect pairing between an introduced TCR α or β chain and an endogenous TCR β or α chain, which results in diluted surface expression of the therapeutic TCR αβ. Although there is currently no clinical evidence for TCR mispairing-induced autoreactivity, the generation of autoreactive TCRs upon TCR mispairing cannot be excluded. So it is important to detect TCR mispairing to evaluate the efficiency of TCR gene therapy. Currently there is no available quantitative assay for the measurement of TCR mispairing. Fluorescence resonance energy transfer (FRET) is a powerful approach for identifying biologically relevant molecular interactions with high spatiotemporal resolution. In this study, we described the method of FRET for the measurement of TCR mispairing. It was found that the average FRET efficiency was 12.2 ± 7.5% in HeLa cells and 8.4 ± 3.3% in Jurkat cells (P = 0.026605). The reduction of FRET efficiency in lymphocytes reflected the presence of mispaired TCRs, indicating there were ~30% TCR mispairing in lymphocytes. This study provides a quantitative intracellular assay that can be used to detect TCR mispairing in genetically modified T lymphocytes.