Epitope Vaccine Research Articles

Immunoinformatic based identification of cytotoxic T lymphocyte epitopes from the Indian isolate of SARS-CoV-2

The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has turned into a pandemic with about thirty million confirmed cases worldwide as of September 2020. Being an airborne infection, it can be catastrophic to populous countries like India. This study sets to identify potential cytotoxic T lymphocyte (CTL) epitopes in the SARS-CoV-2 Indian isolate which can act as an effective vaccine epitope candidate for the majority of the Indian population. The immunogenicity and the foreignness of the epitopes towards the human body have to be studied to further confirm their candidacy. The top-scoring epitopes were subjected to molecular docking studies to study their interactions with the corresponding human leukocyte antigen (HLA) system. The CTL epitopes were observed to bind at the peptide-binding groove of the corresponding HLA system, indicating their potency as an epitope candidate. The candidacy was further analyzed using sequence conservation studies and molecular dynamics simulation. The identified epitopes can be subjected to further studies for the development of the SARS-CoV-2 vaccine.

Structural Analysis of Avian Encephalomyelitis Virus Polyprotein for Development of Multi Epitopes Vaccine Using Immunoinformatics Approach

Avian Encephalomyelitis (AE) is the disease caused by avian encephalomyelitis virus (AEV). The disease mainly affects young birds nervous system worldwide causing high morbidity and variable mortality rate in chicks and noticed egg dropping and hatchability in mature hens. Vaccination is the only way to control AEV infection since there is no treatment yet to the avian encephalomyelitis. This study aimed to use immunoinformatics approaches to predict multi epitopes vaccine from the AEV polyprotein that could elicit both B and T cells. The vaccine construct comprises 482 amino acids obtained from epitopes predicted against B and T cells by IEDB server, adjuvant, linkers and 6-His-tag. The chimeric vaccine was potentially antigenic and nonallergic and demonstrated thermostability and hydrophilicity in protparam server. The solubility of the vaccine was measured in comparison to E. coli proteins. The stability was also assessed by disulfide bonds engineering to reduce the high mobility regions in the designed vaccine. Furthermore molecular dynamics simulation further strengthen stability of the predicted vaccine. Tertiary structure of the vaccine construct after prediction, refinement was used for molecular docking with chicken alleles BF2*2101 and BF2*0401 and the docking process demonstrated favourable binding energy score of -337.47 kcal/mol and -326.87 kcal/mol, respectively. Molecular cloning demonstrated the potential clonability of the chimeric vaccine in pET28a(+) vector. This could guarantee the efficient translation and expression of the vaccine within suitable expression vector.

Prediction and identification of CD4+ T cell epitope for the protective antigens of Mycobacterium tuberculosis.

CD4+T cell epitopes plays a key role in anti-tuberculosis (TB) immunity, CD4+T cell epitopes suitable for the domestic population are lacking. Therefore, we predicted and identified novel CD4+T cell epitopes.The bioinformatics software, namely, DNAStar (DNASTAR of the United States), SYFPEITHI (INTERFACTORS INSTITUT Für ZELL Biologie of Germany), RANKPEP, and NetMHC IIpan (National Cancer Institute, United States of America), were used to comprehensively predict the CD4+T cell immune epitope of Mycobacterium TB, and the predicted epitope polypeptide was synthesized by the standard Fmoc scheme. The proliferation of PBMC and CD4+T cells stimulated by peptides was preliminarily detected by the CCK8 method. Then, the candidate polypeptides screened out by the CCK8 method were verified again by the BrdU assay, and flow cytometry was performed to analyze further the extent of their stimulation on the proliferation of CD4+T cells. The changes in the secreted cytokines IFN-γ, TNF-α, IL-2, and IL-10 before and after the candidate polypeptide stimulation of CD4+T lymphocytes were detected by ELISA. The preliminary humoral immunity test was conducted by indirect ELISA to evaluate the serological diagnostic value of the CD4+T cell epitope polypeptide.In this study, 5 novel candidate CD4+T cell epitope polypeptides with the amino acid sequences of LQGQWRGAAGTAAQA, PVTLAETGSTLLYPL, AAAWGGSGSEAYQGV, QFVYAGAMSGLLDPS, and KAALTRTASNMNAAA and others that have not been reported in the research were predicted. For convenience, the 5 candidates were successively named as P39, P50, P40, P185, and P62. P39, P62, and the mixed peptide P39+P62 could effectively induce the proliferation of CD4+T cells and increase the secretion of IFN-γ, TNF-α, and IL-2 from the CD4+T cells, while reducing the content of IL-10. The serological test showed that the sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) of P39 were 75%, 67.71%, and 0.844, respectively. The sensitivity, specificity, and AUC of P62 were 91.66%, 46.87%, and 0.649, respectively. The sensitivity of the mixed peptide P39+P62 was 95.83%, the specificity was 97.91%, and the AUC was 0.793.The P39 and P62 polypeptides were predicted and identified as potential CD4+T cell immune epitope polypeptides of M. TB. The polypeptide had better diagnosis effect, which provided potential candidate epitope polypeptides for the development of TB-specific diagnosis reagents and novel TB epitope vaccines.

Enhanced epitope immunoreactivity of the dominant epitope of Toxoplasma gondii fused at the "N terminus" of HPV16L1

For improving epitope immunogenicity and achieving the co-immunization, late protein 1 (L1) of HPV type 16 (HPV16L1) was selected as the vector to carry the dominant epitope of Toxoplasma gondii because of the shared common population between Toxoplasma gondii and human papillomavirus (HPV). RSepitope-HPV16L1 (RSepitope fused at the "N-terminus" of HPV16L1) and HPV16L1-RSepitope (RSepitope fused at the "C-terminus" of HPV16L1) chimeras were constructed. After transfection of COS-7 cells with the recombinants, Western blot, RT-PCR, and immunofluorescence experiments confirmed that RSepitope-HPV16L1 could successfully express the corresponding mRNA and protein of RSepitope and HPV16L1, but the HPV16L1-RSepitope construct could not. A "prime-boost" immunization program was applied in mice to further evaluate the immune response elicited by the constructs, and the RSepitope-HPV16L1 immunization group produced the most significantly increased humoral and cellular immune responses (the highest RSepitope-specific IgG antibody level and the highest IFN-γ production, respectively), in which both elevated Th1 and Th2 immune responses were obtained. Moreover, the advantage of HPV16L1 as an epitope carrier was remarkable for RSepitope-HPV16L1, which induced a more prominent immunological response than RSepitope alone (without fusion with HPV16L1). Our research indicated that the N-terminus of HPV16L1 could be a better insertion site for enhancing target epitope immunogenicity, and our study offers a design for epitope vaccine of reasonable combination.

Molecular characterization and epitope-based vaccine predictions for ompA gene associated with biofilm formation in multidrug-resistant strains of A.baumannii.

The present study was conducted to molecularly characterize the biofilm associated ompA gene from the drug resistant strains of A. baumannii and its immuno-dominant vaccine epitope predictions through immuno-informatic approach. ompA was amplified by PCR from the genomic DNA and was sequenced. Using the ORF, ompA protein sequence was retrieved and was subjected for IEDB T cell and B cell epitope analysis for the selection of the epitope peptides. Selected peptides were evaluated using appropriate servers and tools to assess the propensity for its antigenicity, solubility, physico-chemical property, toxigenicity and class-I immunogenicity. MHC class I and II restriction of HLA alleles was also performed. 48% (n = 24) of the strains possessed ompA gene. Protein structure was successfully retrieved with the selection of two epitopes viz., E1- FDGVNRGTRGTSEEGTLGNA and E2-KLSEYPNATARIEGHTDNTGPRKL. Final docking with TLR-2, showed E2 as the best epitope candidate predicted with the highest number of hydrogen bonds.

Glycosylation of SARS-CoV-2 Steers Evolutionary Outcomes in the Postvaccination Phase.

There is a need to assess evolutionary outcomes for SARS-CoV-2 in the postvaccination phase. The role of virus glycosylation in deterring the development of vaccine resistance is weighed against the epitopes of extant vaccines and the modulation of induced immune surveillance on antigens containing glycosylation sites.

Machine Learning and Computational Vaccine-A Novel approach to Vaccine Design against Hepatitis C Virus

Vaccines are molecular entities that are used to invigorate defensive immune system contrary to microbial systems and ailments they produce. Defensive immunity is definitive against pathogens which augment adaptive immune reaction to ensuing re-contagion or, epidemic by accompanying organisms. Such reinforced immunity is interceding by the immune remembrance that imitates counters to the impacts of infectious microorganisms. Designing drug against Hep C virus is not adequate in patients because of delay in gathering information related to disease that finally becomes calamitous due to development of immedicable hepatic cirrhosis. This dilemma can be resolved by crafting peptidal or epitope vaccines, as they have enhanced activity and specificity. The determination of epitopes in non-structural flavivirus 3 protein or P70 provides a suitable primary immune symptomatic antigen for the detection of the HEP C VIRUS. Non-Structural protein epitopes would be predicted in this research work, which could be used as suitable vaccine candidate against Hepatitis C virus infections.

Immunoinformatics designed T cell multi epitope dengue peptide vaccine derived from non structural proteome

Dengue viral disease has been reported as an Aedes aegypti mosquito-borne human disease and causing a severe global public health concern. In this study, immunoinformatics methods was deployed for crafting CTL T-cell epitopes as dengue vaccine candidates. The NS1 protein sequence of dengue serotype 1 strain retrieved from the protein database and T-cell epitopes (n = 85) were predicted by the artificial neural network. The conserved epitopes (n = 10) were predicted and selected for intensive computational analysis. The machine learning technique and quantitative matrix-based toxicity analysis assured nontoxic peptide selection. Hidden Markov Model derived Structural Alphabet (SA) based algorithm predicted the 3D molecular structure and all-atom structure of peptide ligand validated by Ramachandran-plot. Three-tier molecular docking approaches were used to predictthe peptide - HLA docking complex. Molecular dynamics (MD) simulation study confirmed the docking complex was stable in the time frame of 100ns. Population coverage analysis predicted the interaction epitope interaction with a particular population of HLA. These results concluded that the computationally designed HTLWSNGVL and FTTNIWLKL epitope peptides could be used as putative agents for the multi CTL T cell epitope vaccine. The vaccine protein sequence expression and translation were analyzed in the prokaryotic vector adapted by codon usage. Such in silico formulated CTL T-cell-based prophylactic vaccines could encourage the commercial development of dengue vaccines.

Landscape and selection of vaccine epitopes in SARS-CoV-2

Landscape and selection of vaccine epitopes in SARS-CoV-2

Antibodies to neutralising epitopes synergistically block the interaction of the receptor-binding domain of SARS-CoV-2 to ACE 2.

ObjectivesA major COVID‐19 vaccine strategy is to induce antibodies that prevent interaction between the Spike protein's receptor‐binding domain (RBD) and angiotensin‐converting enzyme 2 (ACE2). These vaccines will also induce T‐cell responses. However, concerns were raised that aberrant vaccine‐induced immune responses may exacerbate disease. We aimed to identify minimal epitopes on the RBD that would induce antibody responses that block the interaction of the RBD and ACE2 as a strategy leading to an effective vaccine with reduced risk of inducing immunopathology.MethodsWe procured a series of overlapping 20‐amino acid peptides spanning the RBD and asked which were recognised by plasma from COVID‐19 convalescent patients. Identified epitopes were conjugated to diphtheria‐toxoid and used to vaccinate mice. Immune sera were tested for binding to the RBD and for their ability to block the interaction of the RBD and ACE2.ResultsSeven putative vaccine epitopes were identified. Memory B‐cells (MBCs) specific for one of the epitopes were identified in the blood of convalescent patients. When used to vaccinate mice, six induced antibodies that bound recRBD and three induced antibodies that could partially block the interaction of the RBD and ACE2. However, when the sera were combined in pairs, we observed significantly enhanced inhibition of binding of RBD to ACE2. Two of the peptides were located in the main regions of the RBD known to contact ACE2. Of significant importance to vaccine development, two of the peptides were in regions that are invariant in the UK and South African strains.ConclusionCOVID‐19 convalescent patients have SARS‐CoV‐2‐specific antibodies and MBCs, the specificities of which can be defined with short peptides. Epitope‐specific antibodies synergistically block RBD–ACE2 interaction.

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 (GapC63-77, abbreviated as GT) and two B cell epitopes (GapC30-36, abbreviated as GB1, and GapC97-103, abbreviated as GB2), which were identified in GapC1-150 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 GapC1-150, but higher than that induced by other epitope vaccines. The level of IgG induced by GTB1B2 was lower than that induced by GapC1-150, 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 GapC1-150, 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.

Identification of H7N9 hemagglutinin novel protein epitopes that elicit strong antibody-dependent, cell-mediated cytotoxic activities with protection from influenza infection in mouse model

BackgroundAntibody-dependent cell-mediated cytotoxicity (ADCC) is one of the mechanisms connecting humoral immunity and cellular immunity and has been well-demonstrated in recent studies. Neutralizing antibodies and antibodies can mediate ADCC effects and both build a strong defense against H7N9 influenza virus infection. In our previous study, we found that H7N9 patients’ plasma displayed low neutralizing activities that were not sufficient for host protection; however, the plasma of some patients can mediate strong ADCC effects. MethodsBased on the plasma samples of H7N9 infected patients collected, we measured the ADCC activities of these samples and selected the best to locate the dominant epitopes on H7N9 hemagglutinin (HA) protein that can elicit antibodies and strong ADCC activities. We constructed a yeast surface-display H7N9 HA protein epitope library and screened this library against plasma samples with different potencies in mediating ADCC effects. ResultsTwo dominant epitopes were selected from the screening. Plasma samples with depleted antibodies that were specific to the epitopes showed reduced ADCC activities. The serum of mice immunized with the epitopes elicited strong ADCC activities. Three monoclonal antibodies were isolated which showed high ADCC effects in vitro. Vaccination with isolated ADCC activating epitopes can provide partial protection from influenza infection in mouse model. And mice with vaccinated with combination of epitopes and extracellular domain can provide full protection from influenza infection in the same mouse model. ConclusionsIn this study, the epitopes isolated on H7N9 HA were immunogenic and elicited antibodies and strong ADCC activities in mice. Although the protective effect of the epitopes is partial, the combination of epitopes and extracellular domain can provide 100% protection from influenza virus infection in the same mouse model. Our study provides information on the potential use of epitope vaccine design against H7N9 viral infection.

First identification of B-cell linear epitopes of outer membrane protein A (OmpA) of Edwardsiella anguillarum in rabbit and European eels (Anguilla anguilla)

Epitope vaccine is an important part of vaccine research in the future. However, there is no report about fish epitope vaccine so far. Edwardsiella anguillarum is a new bacterial pathogen and outer membrane protein A (OmpA) of E. anguillarum had been identified as a good antigen. In this study, New Zealand white rabbit and European eels (Anguilla anguilla) were immunized by the recombinant OmpA (rOmpA) after it was expressed and purified. The rabbit serum was collected when the anti-rOmpA serum ELISA titer was 1:40000, then IgG in the rabbit serum was separated by protein-A column affinity chromatography. The theoretical epitopes of the OmpA were analyzed by the ABCpred Prediction Server and 19 B-cell linear epitopes were ascertained, then these epitopes were synthesized and coated on the ELISA plate. Three epitopes were identified by the indirect ELISA using the purified IgG, and 2 epitopes were identified by indirect ELISA when the eel serum was used, then a novel common epitope, VETKRFTLKSDVLFNF (215–230), was found when 19 peptides reacted with rabbit and eel antibodies respectively. The B-cell epitope was identified for the first time using rabbit and fish serum simultaneously, and results of this study will provide reference for fish epitope vaccine design.

Vaccine design based on 16 epitopes of SARS-CoV-2 spike protein.

The global outbreak of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) urgently requires an effective vaccine for prevention. In this study, 66 epitopes containing pentapeptides of SARS‐CoV‐2 spike protein in the IEDB database were compared with the amino acid sequence of SARS‐CoV‐2 spike protein, and 66 potentially immune‐related peptides of SARS‐CoV‐2 spike protein were obtained. Based on the single‐nucleotide polymorphisms analysis of spike protein of 1218 SARS‐CoV‐2 isolates, 52 easily mutated sites were identified and used for vaccine epitope screening. The best vaccine candidate epitopes in the 66 peptides of SARS‐CoV‐2 spike protein were screened out through mutation and immunoinformatics analysis. The best candidate epitopes were connected by different linkers in silico to obtain vaccine candidate sequences. The results showed that 16 epitopes were relatively conservative, immunological, nontoxic, and nonallergenic, could induce the secretion of cytokines, and were more likely to be exposed on the surface of the spike protein. They were both B‐ and T‐cell epitopes, and could recognize a certain number of HLA molecules and had high coverage rates in different populations. Moreover, epitopes 897‐913 were predicted to have possible cross‐immunoprotection for SARS‐CoV and SARS‐CoV‐2. The results of vaccine candidate sequences screening suggested that sequences (without linker, with linker GGGSGGG, EAAAK, GPGPG, and KK, respectively) were the best. The proteins translated by these sequences were relatively stable, with a high antigenic index and good biological activity. Our study provided vaccine candidate epitopes and sequences for the research of the SARS‐CoV‐2 vaccine.

Deciphering the Structural Enigma of HLA Class-II Binding Peptides for Enhanced Immunoinformatics-based Prediction of Vaccine Epitopes.

Vaccines remain the most efficacious means to avoid and eliminate morbid diseases associated with high morbidity and mortality. Clinical trials indicate the gaining impetus of peptide vaccines against diseases for which an effective treatment still remains obscure. CD4 T-cell-based peptide vaccines involve immunization with antigenic determinants from pathogens or neoplastic cells that possess the ability to elicit a robust T helper cell response, which subsequently activates other arms of the immune system. The available in silico predictors of human leukocyte antigen II (HLA-II) binding peptides are sequence-based techniques, which ostensibly have balanced sensitivity and specificity. Structural analysis and understanding of the cognate peptide and HLA-II interactions are essential to empirically derive a successful peptide vaccine. However, the availability of structure-based epitope prediction algorithms is inadequate compared with sequence-based prediction methods. The present study is an attempt to understand the structural aspects of HLA-II binders by analyzing the Protein Data Bank (PDB) complexes of pHLA-II. Furthermore, we mimic the peptide exchange mechanism and demonstrate the structural implication of an acidic environment on HLA-II binders. Finally, we discuss a structure-guided approach to decipher potential HLA-II binders within an antigenic protein. This strategy may accurately predict the peptide epitopes and thus aid in designing successful peptide vaccines.

Graph-theoretical formulation of the generalized epitope-based vaccine design problem.

Epitope-based vaccines have revolutionized vaccine research in the last decades. Due to their complex nature, bioinformatics plays a pivotal role in their development. However, existing algorithms address only specific parts of the design process or are unable to provide formal guarantees on the quality of the solution. We present a unifying formalism of the general epitope vaccine design problem that tackles all phases of the design process simultaneously and combines all prevalent design principles. We then demonstrate how to formulate the developed formalism as an integer linear program, which guarantees optimality of the designs. This makes it possible to explore new regions of the vaccine design space, analyze the trade-offs between the design phases, and balance the many requirements of vaccines.

Strongyloides stercoralis proteome: A reverse approach to the identification of potential immunogenic candidates

Strongyloides stercoralis is a parasite widely distributed in the tropical and subtropical areas in the world. Its treatment and diagnosis have a limitation as many other parasitic diseases. Nowadays, there is a great interest in designing an efficient epitope for vaccines or diagnostic. In this study, a bioinformatics-based screening approach has been incorporated in order to explore potential immunogens in the S. stercoralis proteome. Bioinformatic tools were used to predict diagnostic and vaccinology approaches. 12.851 cell immunology proteins from Uniprot were analyzed. Thirty-four immunogenic candidates were identified, they had higher antigenic activity, less than 2 α-helices, non-allergen activity and they do not have homology with host proteins, all of them have ortholog protein with Strongyloides ratti. Some of them presented a good binding with immunological cell (T and B cell). These proteins could be a good alternative as a candidate for the design of the novel vaccines or diagnostic tests of strongyloides stercoralis.

Immunoinformatics approach to understand molecular interaction between multi-epitopic regions of SARS-CoV-2 spike-protein with TLR4/MD-2 complex.

BackgroundThe coronavirus (CoV) spike (S) protein is critical for receptor binding, membrane fusion and internalization of the virus into the human cells. We have tried to search the epitopic component of the S-protein that might be served as crucial targets for the vaccine development and also tried to understand the molecular mechanism of epitopes and TLR4/MD-2 complex for adaptive immunity.Material and methodsHere we identified the antigenicity and the epitopic divergence of S-protein via immunoinformatics approach. The study was performed to identify the epitopes, composition of amino acids and its distribution in epitopic regions, composition of amino acid between the identified epitopes, secondary structure architecture of epitopes, physicochemical and biochemical parameters and molecular interaction between the identified epitope and TLR4/MD-2 complex. The SARS-CoV-2 can be possibly recognised by TLR4 of host immune cells that are responsible for the adaptive immune response.ResultsWe identified four SARS-CoV-2 S-protein 9mer antigenic epitopes and observed that they bind with the TLR4/MD-2 complex by varied stable molecular bonding interactions. Molecular interaction between these characterized epitopes with TLR4/MD-2 complex might be indicated the binding affinity and downstream signalling of adaptive immune response. Different physicochemical and biochemical parameters such as O-glycosylation and N-glycosylation, Hydrophobicity, GRAVY were identified within epitopic regions of S-protein. These parameters help to understand the protein-protein interaction between epitopes and TLR4/MD-2 complex. The study also revealed different epitopic binding pockets of TLR4/MD-2 complex.ConclusionsThe identified epitopes impart suitable prospects for the development of novel peptide-based epitopic vaccine for the control of COVID-19 infection.

New Immunoinformatics Tools for Swine: Designing Epitope-Driven Vaccines, Predicting Vaccine Efficacy, and Making Vaccines on Demand.

Novel computational tools for swine vaccine development can expand the range of immunization approaches available to prevent economically devastating swine diseases and spillover events between pigs and humans. PigMatrix and EpiCC are two new tools for swine T cell epitope identification and vaccine efficacy analysis that have been integrated into an existing computational vaccine design platform named iVAX. The iVAX platform is already in use for the development of human vaccines, thus integration of these tools into iVAX improves and expands the utility of the platform overall by making previously validated immunoinformatics tools, developed for humans, available for use in the design and analysis of swine vaccines. PigMatrix predicts T cell epitopes for a broad array of class I and class II swine leukocyte antigen (SLA) using matrices that enable the scoring of sequences for likelihood of binding to SLA. PigMatrix facilitates the prospective selection of T cell epitopes from the sequences of swine pathogens for vaccines and permits the comparison of those predicted epitopes with “self” (the swine proteome) and with sequences from other strains. Use of PigMatrix with additional tools in the iVAX toolkit also enables the computational design of vaccines in silico, for testing in vivo. EpiCC uses PigMatrix to analyze existing or proposed vaccines for their potential to protect, based on a comparison between T cell epitopes in the vaccine and circulating strains of the same pathogen. Performing an analysis of T cell epitope relatedness analysis using EpiCC may facilitate vaccine selection when a novel strain emerges in a herd and also permits analysis of evolutionary drift as a means of immune escape. This review of novel computational immunology tools for swine describes the application of PigMatrix and EpiCC in case studies, such as the design of cross-conserved T cell epitopes for swine influenza vaccine or for African Swine Fever. We also describe the application of EpiCC for determination of the best vaccine strains to use against circulating viral variants of swine influenza, swine rotavirus, and porcine circovirus type 2. The availability of these computational tools accelerates infectious disease research for swine and enable swine vaccine developers to strategically advance their vaccines to market.

Promotion of CTL epitope presentation by a nanoparticle with environment-responsive stability and phagolysosomal escape capacity

Vaccines that induce cytotoxic T lymphocyte (CTL)-mediated immune responses constitute an important class of medical tools to fend off diseases like infections and malignancy. Epitope peptides, as a format of CTL vaccines, are being tested preclinically and clinically. To elicit CTL responses, epitope vaccines go through an epitope presentation pathway in dendritic cells (DCs) that has multiple bottleneck steps and hence is inefficient. Here, we report the development of a strategy to overcome one of these barriers, phagolysosomal escape in DCs. First, we furnished a previously established carrier—an immune-tolerant elastin-like polypeptide nanoparticle (iTEP NP)—with the peptides that are derived from the DNA polymerase of herpes simplex virus 1 (Pol peptides). Pol peptides were reported to facilitate phagolysosomal escape. In this study, while we found that Pol peptides promoted the CTL epitope presentation; we also discovered Pol peptides disrupted the formation of the iTEP NP. Thus, we engineered a series of new iTEPs and identified several iTEPs that could accommodate Pol peptides and maintain their NP structure at the same time. We next optimized one of these NPs so that its stability is responsive to its redox environment. This environment-responsive NP further strengthened the CTL epitope presentation and CTL responses. Lastly, we revealed how this NP and Pol peptides utilized biological cues of phagolysosomes to realize phagolysosomal escape and epitope release. In summary, we developed iTEP NP carriers with a new phagolysosomal escape function. These carriers, with their priorly incorporated functions, resolve three bottleneck issues in the CTL epitope presentation pathway: vaccine uptake, phagolysosomal escape, and epitope release.