DNA vaccine with discontinuous T-cell epitope insertions into HSP65 scaffold as a potential means to improve immunogenicity of multi-epitope Mycobacterium tuberculosis vaccine

DNA and RNA vaccines against tuberculosis: a scoping review of human and animal studies

Introduction

To comprehensively identify and provide an overview of in vivo or clinical studies of nucleic acids (NA)-based vaccines against TB we included human or animal studies of NA vaccines for the prevention or treatment of TB and excluded in vitro or in silico research, studies of microorganisms other than M. tuberculosis, reviews, letters, and low-yield reports.

Methods

We searched PubMed, Scopus, Embase, selected Web of Science and ProQuest databases, Google Scholar, eLIBRARY.RU, PROSPERO, OSF Registries, Cochrane CENTRAL, EU Clinical Trials Register, clinicaltrials.gov, and others through WHO International Clinical Trials Registry Platform Search Portal, AVMA and CABI databases, bioRxiv, medRxiv, and others through OSF Preprint Archive Search. We searched the same sources and Google for vaccine names (GX-70) and scanned reviews for references. Data on antigenic composition, delivery systems, adjuvants, and vaccine efficacy were charted and summarized descriptively.

Results

A total of 18,157 records were identified, of which 968 were assessed for eligibility. No clinical studies were identified. 365 reports of 345 animal studies were included in the review. 342 (99.1%) studies involved DNA vaccines, and the remaining three focused on mRNA vaccines. 285 (82.6%) studies used single-antigen vaccines, while 48 (13.9%) used multiple antigens or combinations with adjuvants. Only 12 (3.5%) studies involved multiepitope vaccines. The most frequently used antigens were immunodominant secretory antigens (Ag85A, Ag85B, ESAT6), heat shock proteins, and cell wall proteins. Most studies delivered naked plasmid DNA intramuscularly without additional adjuvants. Only 4 of 17 studies comparing NA vaccines to BCG after M. tuberculosis challenge demonstrated superior protection in terms of bacterial load reduction. Some vaccine variants showed better efficacy compared to BCG.

Systematic review registration

https://osf.io/, identifier F7P9G.

Structural vaccinology-based design of multi-epitopes vaccine against Streptococcus gordonii and validation using molecular modeling and immune simulation approaches

Streptococcus gordonii is an oral bacterium colonizing the dental cavity and leading to plaque formation. This pervasive colonizer is also the etiologic agent of bacterial endocarditis and has a major role in infective endocarditis. The bacteria reach the heart through oral bleeding, leading to inflammation of cardiovascular valves. Over the past 50 years, it has shown a significant pathogenic role in immunocompromised and neutropenic patients. Since antibiotic resistance has created prophylaxis failure towards infective endocarditis, a potent therapeutic candidate is needed. Therefore, multi-epitopes vaccine offers advantages over the other approaches. Thus, herein, numerous molecular-omics tools were exploited to mine immunogenic peptides, i.e., T-cell and B-cell epitopes, and construct a vaccine sequence. Our findings revealed a total of 24 epitopes, including CTL, HTL, and B-cell are responsible for imparting immune responses, which were combined with the help of different linkers, and MEVC was constructed. Multifactorial validation of the candidate vaccine was performed to minimize the risk factors. The final sequence was docked with TLR2 to validate its conformation compatibility with receptor and long-term interactions stability. Our analysis revealed that the vaccine construct is immunogenic and non-allergenic. The construct also established various contacts with the immune receptor. Finally, the vaccine sequence was reverse-translated, optimized for codon usage, and analyzed for expression in the Escherichia coli K12 strain. Maximum expression was noted with a CAI score of 0.95. In silico immune simulation revealed that the antigen was neutralized on the 3rd day after injection. In conclusion, the current study warrants validation of the vaccine construct both in in vitro and in vivo models for accurate therapeutic intervention.

Mechanisms of a Mycobacterium tuberculosis Active Peptide

Multidrug-resistant tuberculosis (MDR) continues to pose a threat to public health. Previously, we identified a cationic host defense peptide with activity against Mycobacterium tuberculosis in vivo and with a bactericidal effect against MDR M. tuberculosis at therapeutic concentrations. To understand the mechanisms of this peptide, we investigated its interactions with live M. tuberculosis and liposomes as a model. Peptide interactions with M. tuberculosis inner membranes induced tube-shaped membranous structures and massive vesicle formation, thus leading to bubbling cell death and ghost cell formation. Liposomal studies revealed that peptide insertion into inner membranes induced changes in the peptides' secondary structure and that the membranes were pulled such that they aggregated without permeabilization, suggesting that the peptide has a strong inner membrane affinity. Finally, the peptide targeted essential proteins in M. tuberculosis, such as 60 kDa chaperonins and elongation factor Tu, that are involved in mycolic acid synthesis and protein folding, which had an impact on bacterial proliferation. The observed multifaceted targeting provides additional support for the therapeutic potential of this peptide.

Nanomaterials in tuberculosis DNA vaccine delivery: historical perspective and current landscape

Vaccinations, especially DNA vaccines that promote host immunity, are the most effective interventions for tuberculosis (TB) control. However, the vaccine delivery system exhibits a significant impact on the protective effects of the vaccine. Recently, effective nanomaterial-based delivery systems (including nanoparticles, nanogold, nanoliposomes, virus-like particles, and virus carriers) have been developed for DNA vaccines to control TB. This review highlights the historical development of various nanomaterial-based delivery systems for TB DNA vaccines, along with the emerging technologies. Nanomaterial-based vaccine delivery systems could enhance the efficacy of TB vaccination; therefore, this summary could guide nanomaterial selection for optimal and safe vaccine delivery, facilitating the design and development of highly effective TB vaccines.

Peptide-Based Vaccines for Tuberculosis

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis. As a result of the coronavirus disease 2019 (COVID-19) pandemic, the global TB mortality rate in 2020 is rising, making TB prevention and control more challenging. Vaccination has been considered the best approach to reduce the TB burden. Unfortunately, BCG, the only TB vaccine currently approved for use, offers some protection against childhood TB but is less effective in adults. Therefore, it is urgent to develop new TB vaccines that are more effective than BCG. Accumulating data indicated that peptides or epitopes play essential roles in bridging innate and adaptive immunity and triggering adaptive immunity. Furthermore, innovations in bioinformatics, immunoinformatics, synthetic technologies, new materials, and transgenic animal models have put wings on the research of peptide-based vaccines for TB. Hence, this review seeks to give an overview of current tools that can be used to design a peptide-based vaccine, the research status of peptide-based vaccines for TB, protein-based bacterial vaccine delivery systems, and animal models for the peptide-based vaccines. These explorations will provide approaches and strategies for developing safer and more effective peptide-based vaccines and contribute to achieving the WHO's End TB Strategy.

Evaluation of the immune response to a multi-epitope vaccine candidate in comparison with HlaH35L, MntC, and SACOL0723 proteins against MRSA infection

Staphylococcus aureus is an important human opportunistic pathogen that can have a major influence on public health. Here, we aimed to evaluate different aspects of the immune response to a novel multi-epitope fusion protein (HMS) based on Hla_H35L, MntC, and SACOL0723 proteins in comparison to the individual antigens. For this purpose, specific total IgG, IgG1, and IgG2a isotypes and the cytokines related to Th1, Th2, and Th17 were assessed. The Bio-efficiency of the fusion protein was evaluated by opsonic killing activity. The HMS fusion protein elicited a high specific IgG level and also induced a higher level of Th1, Th2, and Th17-related cytokines which were more polarized towards the Th1 and Th17 compared to individual antigens. The HMS-specific antisera also significantly promoted phagocytosis of S. aureus COL strain by mouse macrophages. In conclusion, the fusion protein might be an effective vaccine for potential protective immunity against a lethal infection of S. aureus in mice.

Immunogenicity of multi-epitope vaccines composed of epitopes from Streptococcus dysgalactiae GapC

Glyceraldehyde-3-phosphate dehydrogenase C (GapC) of Streptococcus dysgalactiae (S. dysgalactiae) is a highly conserved surface protein that can induce a protective immune response against S. dysgalactiae infection. To investigate the immune response and protective efficacy induced by epitope-vaccines against S. dysgalactiae infection, we constructed epitope-vaccines GTB1, GB1B2, and GTB1B2 using a T cell epitope (GapC_63-77, abbreviated as GT) and two B cell epitopes (GapC_30-36, abbreviated as GB1, and GapC_97-103, abbreviated as GB2), which were identified in GapC_1-150 of S. dysgalactiae in tandem by a GSGSGS linker. BALB/c mice were immunized via an intramuscular injection with the epitope vaccines. The levels of the cytokines, IFN-γ, IL-4, and IL-17, secreted by splenic lymphocytes and the antibody levels in the sera of the immunized mice were detected by ELISA. The immunized mice were subsequently challenged with S. dysgalactiae, and the bacterial colonization in the immunized-mouse organs was examined using the plate counting method. The results showed that the level of the cytokines induced by GTB1B2 was lower than that induced by GapC_1-150, but higher than that induced by other epitope vaccines. The level of IgG induced by GTB1B2 was lower than that induced by GapC_1-150, but higher than the levels induced by other epitope vaccines. The bacterial colonization numbers in the organs of the mice immunized with GTB1B2 were higher those of the mice immunized with GapC_1-150, but significantly lower than those from the mice immunized with other epitope-vaccines. Our results demonstrated that the T cell and B cell epitopes in the epitope-vaccines worked synergistically against bacterial challenge. The multi-epitope vaccine, GTB1B2, could induce stronger cellular and humoral immune responses, and provide a better protective effect against S. dysgalactiae infection.

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.

Extensive immunoinformatics study for the prediction of novel peptide-based epitope vaccine with docking confirmation against envelope protein of Chikungunya virus: a computational biology approach

Chikungunya virus (CHIKV) instigating Chikungunya fever is a global infective menace resulting in high fever, weakened joint-muscle pain, and brain inflammation. Inaccessibility and unavailability of effective drugs have led us to an uncertain arena when it comes to providing proper medical treatment to the affected people. In this study, authentic encroachment has been made concerning the peptide-based epitope vaccine designing against CHIKV. A Proteome-wide search was performed to locate a conserved portion among the accessible viral outer membrane proteins which showcase a remarkable immune response using specific immunoinformatics and docking simulation tools. Primarily, the most probable immunogenic envelope glycoproteins E1 and E2 were identified from the UniProt database depending on their antigenicity scores. Subsequently, we selected two distinctive sequences "SEDVYANTQLVLQRP" and "IMLLYPDHPTLLSYR" in both E1 and E2 glycoproteins respectively. These two sequences identified as the most potent T and B cell epitope-based peptides as they interacted with 6 and 7 HLA-I and 5 HLA-II molecules with an extremely low IC50 score that was verified by molecular docking. Moreover, the sequences possess no allergenicity and are certainly located outside the transmembrane region. In addition, the sequences exhibited 88.46% and 100.00% Conservancy, covering high population coverage of 89.49% to 94.74% and 60.51% to 88.87% respectively in endemic countries. The identified peptide SEDVYANTQLVLQRP and IMLLYPDHPTLLSYR can be utilized next for the development of peptide-based epitope vaccine contrary to CHIKV, so further documentations and experimentations like Antigen testing, Antigen production, Clinical trials are needed to prove the validity of it. Communicated by Ramaswamy H. Sarma.

Bioinformatics analysis and epitope screening of a potential vaccine antigen TolB from Acinetobacter baumannii outer membrane protein

The clinical isolation rate of multidrug-resistant or pan-resistant Acinetobacter baumannii (A. baumannii) is increasing, resulting that optional antibiotics are very limited in clinical practice. To deal with such a dilemma in treatment, the development of effective vaccines serves as a good strategy. Outer membrane proteins (Omp) often contain potential excellent vaccine antigens, and NCBI has published >300 Omp sequences of A. baumannii (including the duplicates). To accurately screen out the potential excellent antigen molecules from a large number of sequences, and avoid repetitive experimental processes is of great significance. In this study, we used the bioinformatics software to give extensive predictions of TolB protein. Results suggest it is a potential vaccine antigen. We then cloned the TolB gene fragments and confirmed it was highly conserved among the strains. Finally, we designed a good recombinant epitopes and conducted experimental verification. These findings provided grounds for animal immunology experiments in the future, and showed an orientation for the efficient development of A. baumannii vaccine.

Protective Vaccine Efficacy of the Complete Form of PPE39 Protein from Mycobacterium tuberculosis Beijing/K Strain in Mice

The aim of this study was to evaluate the protective efficacy of MTBK_24820, a complete form of PPE39 protein derived from a predominant Beijing/K strain of Mycobacterium tuberculosis in South Korea. Mice were immunized with MTKB_24820, M. bovis Bacilli Calmette-Guérin (BCG), or adjuvant prior to a high-dosed Beijing/K strain aerosol infection. After 4 and 9 weeks, bacterial loads were determined and histopathologic and immunologic features in the lungs and spleens of the M. tuberculosis-infected mice were analyzed. Putative immunogenic T-cell epitopes were examined using synthetic overlapping peptides. Successful immunization of MTBK_24820 in mice was confirmed by increased IgG responses (P < 0.05) and recalled gamma interferon (IFN-γ), interleukin-2 (IL-2), IL-6, and IL-17 responses (P < 0.05 or P < 0.01) to MTBK_24820. After challenge with the Beijing/K strain, an approximately 0.5 to 1.0 log₁₀ reduction in CFU in lungs and fewer lung inflammation lesions were observed in MTBK_24820-immunized mice compared to those for control mice. Moreover, MTBK_24820 immunization elicited significantly higher numbers of CD4⁺ T cells producing protective cytokines, such as IFN-γ and IL-17, in lungs and spleens (P < 0.01) and CD4⁺ multifunctional T cells producing IFN-γ, tumor necrosis factor alpha (TNF-α), and/or IL-17 (P < 0.01) than in control mice, suggesting protection comparable to that of BCG against the hypervirulent Beijing/K strain. The dominant immunogenic T-cell epitopes that induced IFN-γ production were at the N terminus (amino acids 85 to 102 and 217 to 234). Its vaccine potential, along with protective immune responses in vivo, may be informative for vaccine development, particularly in regions where the M. tuberculosis Beijing/K-strain is frequently isolated from TB patients.

Intranasal Vaccination with Mannosylated Chitosan Formulated DNA Vaccine Enables Robust IgA and Cellular Response Induction in the Lungs of Mice and Improves Protection against Pulmonary Mycobacterial Challenge

Induction of specific humoral and cellular immunity in the lung airways is proposed to be critical for vaccine protection against Mycobacterium tuberculosis (M. tb). To facilitate airway delivery and antigen targeting to the antigen presenting cells in the alveoli, we employed mannosylated chitosan (MCS) to formulate a multi-T-epitope DNA vaccine, pPES, as an intranasal TB vaccine. MCS-DNA nanoparticles appeared spherical with the average particle sizes as 400 nm. HSP65-specific bronchoalveolar lavage fluid SIgA level was significantly elevated by 4 doses of MCS-pPES intranasal immunization as compared to chitosan (CS)-DNA and BCG vaccine. I.n. immunization with MCS-DNA induced a modest peptide-specific Th1(IFN-γ, TNF-α, and IL-2) response in the spleen, while a potent poly-functional CD4+ T response that largely produced TNF-α and IFN-γ, as well as IL-2 in the lung, qualitatively better than that induced by CS-DNA and BCG vaccination. Such response by i.n. immunization with MCS-DNA provided improved protection in the lung against airway Mycobacterial bovis BCG challenge over i.n. CS-DNA and DNA, that is comparable to protection achieved by s.c. BCG vaccination. This enhanced protection was correlated with much greater accessibility of DNA particles to the alveolar macrophages in the lung mediated by man-chitosan. Thus, man-chitosan TB vaccine represents a promising vaccine platform capable of eliciting robust multi-functional T response in the lung mucus and achieving enhanced mucosal immune protection against pulmonary TB.

Vaccination with a Paramyosin-Based Multi-Epitope Vaccine Elicits Significant Protective Immunity against Trichinella spiralis Infection in Mice

Trichinellosis is a worldwide zoonosis and remains a serious public health problem. Interrupting parasite transmission via vaccination of livestocks with a potent vaccine is a practical approach to prevent human Trichinellosis. Our previous studies have identified that paramyosin of Trichinella spiralis (Ts-Pmy) is a good vaccine candidate against Trichinellosis. In this study, a novel multi-epitope vaccine (MEP) was constructed by using four CD4⁺ T cell epitopes (P2, P3, P4, and P5) and one B cell epitope (YX1) from Ts-Pmy and expressed as a soluble recombinant protein (rMEP) in Escherichia coli. Mice immunized with rMEP vaccine produced significant higher muscle larval reduction (55.4%) than that induced by immunization of parental rTs-Pmy (34.4%) against T. spiralis infection. The better protection is associated with rMEP induced high levels of anti-rMEP specific IgG and subclass IgG1/IgG2a, elevated T cell proliferation of splenocytes and secretion of IFN-γ, IL-4 and IL-5. The cellular response to individual T cell epitope also showed that splenocytes from mice immunized with rMEP strongly response to the stimulation of synthetic epitope peptide P2, P3, and P4, but not to P5, suggesting that most of T cell epitopes are exposed and processed well during immunization that may contribute to the high protection induced by the immunization of rMEP. This study implies that epitope vaccine is a promising approach for the development of vaccines against Trichinellosis.

Immunogenicity of a Multi-Epitope DNA Vaccine Encoding Epitopes from Cu-Zn Superoxide Dismutase and Open Reading Frames of Brucella abortus in Mice

Brucellosis is a bacterial zoonotic disease affecting several mammalian species that is transmitted to humans by direct or indirect contact with infected animals or their products. In cattle, brucellosis is almost invariably caused by Brucella abortus. Live, attenuated Brucella vaccines are commonly used to prevent illness in cattle, but can cause abortions in pregnant animals. It is, therefore, desirable to design an effective and safer vaccine against Brucella. We have used specific Brucella antigens that induce immunity and protection against B. abortus. A novel recombinant multi-epitope DNA vaccine specific for brucellosis was developed. To design the vaccine construct, we employed bioinformatics tools to predict epitopes present in Cu-Zn superoxide dismutase and in the open reading frames of the genomic island-3 (BAB1_0260, BAB1_0270, BAB1_0273, and BAB1_0278) of Brucella. We successfully designed a multi-epitope DNA plasmid vaccine chimera that encodes and expresses 21 epitopes. This DNA vaccine induced a specific humoral and cellular immune response in BALB/c mice. It induced a typical T-helper 1 response, eliciting production of immunoglobulin G2a and IFN-γ particularly associated with the Th1 cell subset of CD4+ T cells. The production of IL-4, an indicator of Th2 activation, was not detected in splenocytes. Therefore, it is reasonable to suggest that the vaccine induced a predominantly Th1 response. The vaccine induced a statistically significant level of protection in BALB/c mice when challenged with B. abortus 2308. This is the first use of an in silico strategy to a design a multi-epitope DNA vaccine against B. abortus.