pstS1 polymorphisms of Mycobacterium tuberculosis strains may reflect ongoing immune evasion

Modeling of MT. P495, an mRNA-based vaccine against the phosphate-binding protein PstS1 of Mycobacterium tuberculosis

Tuberculosis (TB) is a contagious disease that predominantly affects the lungs, but can also spread to other organs via the bloodstream. TB affects about one-fourth population of the world. With age, the effectiveness of Bacillus Calmette-Guérin (BCG), the only authorized TB vaccine, decreases. In the quest for a prophylactic and immunotherapeutic vaccine, in this study, a hypothetical mRNA vaccine is delineated, named MT. P495, implementing in silico and immunoinformatics approaches to evaluate key aspects and immunogenic epitopes across the PstS1, a highly conserved periplasmic protein of Mycobacterium tuberculosis (Mtb). PstS1 elicited the potential to generate 99.9% population coverage worldwide. The presence of T- and B-cell epitopes across the PstS1 protein were validated using several computational prediction tools. Molecular docking and dynamics simulation confirmed stable epitope-allele interaction. Immune cell response to the antigen clearance rate was verified by the in silico analysis of immune simulation. Codon optimization confirmed the efficient translation of the mRNA in the host cell. With Toll-like receptors, the vaccine exhibited stable and strong interactions. Findings suggest that the MT. P495 vaccine probably will elicit specific immune responses against Mtb. This mRNA vaccine model is a ready source for further wet-lab validation to confirm the efficacy of this proposed vaccine candidate.

A Multistage Antigen Complex Epera013 Promotes Efficient and Comprehensive Immune Responses in BALB/c Mice

Tuberculosis (TB) remains a serious global health problem. Despite the widespread use of the Mycobacterium bovis bacillus Calmette-Guerin (BCG) vaccine, the primary factor for the TB pandemic and deaths is adult TB, which mainly result from endogenous reactivation of latent Mycobacterium tuberculosis (MTB) infection. Improved new TB vaccines with eligible safety and long-lasting protective efficacy remains a crucial step toward the prevention and control of TB. In this study, five immunodominant antigens, including three early secreted antigens and two latency associated antigens, were used to construct a single recombinant fusion protein (Epera013f) and a protein mixture (Epera013m). When formulated with aluminum adjuvant, the two subunit vaccines Epera013m and Epera013f were administered to BALB/c mice. The humoral immune responses, cellular responses and MTB growth inhibiting capacity elicited after Epera013m and Epera013f immunization were analyzed. In the present study, we demonstrated that both the Epera013f and Epera013m were capable of inducing a considerable immune response and protective efficacy against H37Rv infection compared with BCG groups. In addition, Epera013f generated a more comprehensive and balanced immune status, including Th1, Th2 and innate immune response, over Epera013f and BCG. The multistage antigen complex Epera013f possesses considerable immunogenicity and protective efficacy against MTB infection ex vivo indicating its potential and promising applications in further TB vaccine development.

Design of multi-epitope based vaccine against Mycobacterium tuberculosis: a subtractive proteomics and reverse vaccinology based immunoinformatics approach

Tuberculosis is an airborne transmissible disease caused by Mycobacterium tuberculosis that infects millions of lives worldwide. There is still no single comprehensive therapy or preventative available for the lethal illness. Currently, the available vaccine, BCG is ineffectual in preventing the prophylactic adult pulmonary TB and reactivation of latent tuberculosis. Therefore, this investigation was intended to design a new multi-epitope vaccine that can address the existing problems. The subtractive proteomics approach was implemented to prioritize essential, virulence, druggable, and antigenic proteins as suitable vaccine candidates. Furthermore, a reverse vaccinology-based immunoinformatics technique was employed to identify potential B-cell, helper T lymphocytes (HTL), and cytotoxic T lymphocytes (CTL) epitopes from the target proteins. Immune-stimulating adjuvant, linkers, and PADRE (Pan HLA-DR epitopes) amino acid sequences along with the selected epitopes were used to construct a chimeric multi-epitope vaccine. The molecular docking and normal mode analysis (NMA) were carried out to evaluate the binding mode of the designed vaccine with different immunogenic receptors (MHC-I, MHC-II, and Tlr4). In addition, the MD simulation, followed by essential dynamics study and MMPBSA analysis, was carried out to understand the dynamics and stability of the complexes. In-silico cloning was accomplished using E.coli as an expression system to express the designed vaccine successfully. Finally, the immune simulation study has foreseen that our designed vaccine could induce a significant immune response by elevation of different immunoglobulins in the host. However, there is an imperative need for the experimental validation of the designed vaccine in animal models to confer effectiveness and safety.HIGHLIGHTSMulti-epitope based vaccine was designed against Mycobacterium tuberculosis using subtractive proteomics and Immunoinformatics approach.The vaccine was found to be antigenic, non-allergenic, immunogenic, and stable based on in-silico prediction.Population coverage analysis of the proposed vaccine predicts an effective response in the world population.The molecular docking, MD simulation, and MM-PBSA study confirm the stable interaction of the vaccine with immunogenic receptors.In silico cloning and immune simulation of the vaccine demonstrated its successful expression in E.coli and induction of immune response in the host. Communicated by Ramaswamy H. Sarma.

A real-time PCR assay based on a specific mutation of PstS1 gene for detection of M. bovis strains

The Mycobacterium tuberculosis complex (MTBC) is composed of several genetically related and pathogenic mycobacterial species, including M. tuberculosis, M. bovis and M.africanum et al. In our previous study, we found that M. bovis strains had a unique SNP located in position 1055 in the sequence of the pstS1 gene in which a T was substituted by a C. In this study, specific primers and MGB probes were designed according to the mutation in PstS1 gene, and a sensitive, specific and rapid real-time PCR assay for M. bovis was established. Then the assay was used to detect M. bovis in simulation samples. The minimum detectable concentration is 10¹ copies for M. bovis DNA. The standard curve showed correlation coefficient between threshold cycle and PstS1 gene fragment copy number was 0.997 and slope is -3.144. The minimum detectable concentration is 10¹ cells/ml for simulation sample. In addition, M.bovis strain 93006, 14 clinical BCG stains and 7 clinical M.bovis strain showed positive while the other strains showed negative results, which proved good specificity. This assay had high sensitivity and specificity for identification of M. bovis from the simulation specimens. The assay can be applied for epidemiological and ecological surveillance of M. bovis strains.

Polymorphism of MPT64 and PstS1 in Mycobacterium tuberculosis is not likely to affect relative immune reaction in human

BACKGROUND

MPT64 and PstS1 are the earliest known immune-dominant antigens of Mycobacterium tuberculosis and have been commonly used as candidates in the diagnosis of tuberculosis.

METHODS

We constructed recombinant plasmids pET-32a-Rv0934 and pET-32a-Rv1980c to express both wild and mutant forms of MPT64 and PstS1 and purified them. From November 9 to December 9, 2016, and November 9 to December 10, 2017, 96 patients with tuberculosis, 53 patients without tuberculosis, and 96 healthy volunteers were enrolled in this study. We used the purified proteins as antigens to perform T-spot and enzyme-linked immunosorbent assay (ELISA) for samples obtained from healthy volunteers and tuberculosis patients.

RESULTS

Regarding T-spot, the area under the curve (AUC) values for MPT64-wild protein (MPT64-H37Rv) and MPT64-mutant protein (MPT64-FJ05395) were 0.723 and 0.750, respectively. The AUC values for PstS1-H37Rv, PstS1-FJ05132, and PstS1-JL06035 were 0.817, 0.796, and 0.745, respectively. With regard to ELISA, the AUC values for MPT64-H37Rv and MPT64-FJ05395 were 0.525 and 0.528, respectively, while those for PstS1-H37Rv, PstS1-FJ05132, PstS1-JL06035 were 0.588, 0.509, and 0.560, respectively. There was no difference between wild and mutant proteins when we used them as antigens to perform T-spot and ELISA assays.

CONCLUSION

MPT64 and PstS1 are likely candidate diagnostic antigens for M tuberculosis T-spot test, at least in combination with other proteins. Polymorphisms of MPT64 and PstS1 had little effect on cell-mediated and humoral immunity in the host.

Polymorphisms of human T cell epitopes of Mycobacterium tuberculosis indicate divergence of host immune pressure on different categories of proteins

Mycobacterium tuberculosis is the most successful pathogen with multiple mechanisms to subvert host immune response, resulting in insidious disease. There are few studies on whether the bacteria undergo antigenic variation in response to host immune pressure. Studies on T cell epitopes of M. tuberculosis can help us further understand the mechanism of interaction between the bacteria and host immune system. Here, we selected 180 M. tuberculosis complex in China, amplified 462 experimentally verified human T cell epitopes, sequenced and compared the results to analyze the diversity of those epitopes. It proved that a large majority human T cell epitopes of M. tuberculosis are conserved. However, polymorphisms of T cell epitopes indicated different categories of proteins suffered divergence from host immune pressure. Moreover, Beijing strains are more conservative than non-Beijing strains in T cell epitopes, which might make them easier to transmit than non-Beijing strains.

Genetic diversity of antigen 38 kDa in Mycobacterium tuberculosis strains from China

We used 335 Mycobacterium tuberculosis strains from 2010 National Epidemiologic Survey for TB in China and performed comparative sequence analysis of 38 kDa gene after amplification. From the results, we found that there were 5.07% M.tuberculosis strains that demonstrated genetic diversity of 38 kDa in China, and 2.99% strains showed polymorphism of the 38 kDa antigen, and this may be the reason for changes in the antigen produced, which may in turn cause alterations of related functions, thereby allowing immune evasion.

Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition

The advent of whole-genome sequencing has provided an unprecedented detail about the evolution and genetic significance of species-specific variations across the whole Mycobacterium tuberculosis Complex. However, little attention has been focused on understanding the functional roles of these variations in the protein coding sequences. In this work, we compare the coding sequences from 74 sequenced mycobacterial species including M. africanum, M. bovis, M. canettii, M. caprae, M. orygis, and M. tuberculosis. Results show that albeit protein variations affect all functional classes, those proteins involved in lipid and intermediary metabolism and respiration have accumulated mutations during evolution. To understand the impact of these mutations on protein functionality, we explored their implications on protein ductility/disorder, a yet unexplored feature of mycobacterial proteomes. In agreement with previous studies, we found that a Gly71Ile substitution in the PhoPR virulence system severely affects the ductility of its nearby region in M. africanum and animal-adapted species. In the same line of evidence, the SmtB transcriptional regulator shows amino acid variations specific to the Beijing lineage, which affects the flexibility of the N-terminal trans-activation domain. Furthermore, despite the fact that MTBC epitopes are evolutionary hyperconserved, we identify strain- and lineage-specific amino acid mutations affecting previously known T-cell epitopes such as EsxH and FbpA (Ag85A). Interestingly, in silico studies reveal that these variations result in differential interaction of epitopes with the main HLA haplogroups.

The Case for Live Attenuated Vaccines against the Neglected Zoonotic Diseases Brucellosis and Bovine Tuberculosis

Vaccination of humans and animals with live attenuated organisms has proven to be an effective means of combatting some important infectious diseases. In fact, the 20th century witnessed tremendous improvements in human and animal health worldwide as a consequence of large-scale vaccination programs with live attenuated vaccines (LAVs). Here, we use the neglected zoonotic diseases brucellosis and bovine tuberculosis (BTb) caused by Brucella spp. and Mycobacterium bovis (M. bovis), respectively, as comparative models to outline the merits of LAV platforms with emphasis on molecular strategies that have been pursued to generate LAVs with enhanced vaccine safety and efficacy profiles. Finally, we discuss the prospects of LAV platforms in the fight against brucellosis and BTb and outline new avenues for future research towards developing effective vaccines using LAV platforms.

The microbiome at the pulmonary alveolar niche and its role in Mycobacterium tuberculosis infection

Advances in next generation sequencing (NGS) technology have provided the tools to comprehensively and accurately characterize the microbial community in the respiratory tract in health and disease. The presence of commensal and pathogenic bacteria has been found to have important effects on the lung immune system. Until relatively recently, the lung has received less attention compared to other body sites in terms of microbiome characterization, and its study carries special technological difficulties related to obtaining reliable samples as compared to other body niches. Additionally, the complexity of the alveolar immune system, and its interactions with the lung microbiome, are only just beginning to be understood. Amidst this complexity sits Mycobacterium tuberculosis (Mtb), one of humanity's oldest nemeses and a significant public health concern, with millions of individuals infected with Mtb worldwide. The intricate interactions between Mtb, the lung microbiome, and the alveolar immune system are beginning to be understood, and it is increasingly apparent that improved treatment of Mtb will only come through deep understanding of the interplay between these three forces. In this review, we summarize our current understanding of the lung microbiome, alveolar immunity, and the interaction of each with Mtb.

Single nucleotide polymorphism in Ag85 genes of Mycobacterium tuberculosis complex: analysis of 178 clinical isolates from China and 13 BCG strains

Host immune pressure and associated immune evasion of pathogenic bacteria are key features of host-pathogen co-evolution. Human T-cell epitopes of Mycobacterium tuberculosis (M. tuberculosis) were evolutionarily hyperconserved and thus it was deduced that M. tuberculosis lacks antigenic variation and immune evasion. However, in our previous studies, proteins MPT64, PstS1, Rv0309 and Rv2945c all harbored higher numbers of amino acid substitutions in their T cell epitopes, which suggests their roles in ongoing immune evasion. Here, we used the same set of 180 clinical M. tuberculosis complex (MTBC) isolates from China, amplified the genes encoding Ag85 complex, and compared the sequences. The results showed that Ag85 were hyperconserved in T/B cell epitopes and the genes were more likely to be under purifying selection. The divergence of host immune selection on different proteins may result from different function of the proteins. In addition, A312G of Ag85A and T418C of Ag85B may represent special mutations in BCG strains, which may be used to differentiate M.bovis and BCG strains from MTB strains. Also, C714A in Ag85B seems to be a valuable phylogenetic marker for Beijing strains.