Prediction and In Silico Identification of Novel B-Cells and T-Cells Epitopes in the S1-Spike Glycoprotein of M41 and CR88 (793/B) Infectious Bronchitis Virus Serotypes for Application in Peptide Vaccines

Bioinformatic analysis was used to predict antigenic B-cell and T-cell epitopes within the S1 glycoprotein of M41 and CR88 IBV strains. A conserved linear B-cell epitope peptide, YTSNETTDVTS175–185, was identified in M41 IBV strains while three such epitopes types namely, VSNASPNSGGVD279–290, HPKCNFRPENI328–338, and NETNNAGSVSDCTAGT54–69, were predicted in CR88 IBV strains. Analysis of MHCI binding peptides in M41 IBV strains revealed the presence of 15 antigenic peptides out of which 12 were highly conserved in 96–100% of the total M41 strains analysed. Interestingly three of these peptides, GGPITYKVM208, WFNSLSVSI356, and YLADAGLAI472, relatively had high antigenicity index (>1.0). On the other hand, 11 MHCI binding epitope peptides were identified in CR88 IBV strains. Of these, five peptides were found to be highly conserved with a range between 90% and 97%. However, WFNSLSVSL358, SYNISAASV88, and YNISAASVA89 peptides comparably showed high antigenicity scores (>1.0). Combination of antigenic B-cells and T-cells peptides that are conserved across many strains as approach to evoke humoral and CTL immune response will potentially lead to a broad-based vaccine that could reduce the challenges in using live attenuated vaccine technology in the control of IBV infection in poultry.

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Swine T-Cells and Specific Antibodies Evoked by Peptide Dendrimers Displaying Different FMDV T-Cell Epitopes

Frontiers in Immunology ◽

10.3389/fimmu.2020.621537 ◽

2021 ◽

Vol 11 ◽

Author(s):

Patricia de León ◽

Rodrigo Cañas-Arranz ◽

Sira Defaus ◽

Elisa Torres ◽

Mar Forner ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

B Cell ◽

Cell Epitope ◽

T Cell Epitope ◽

T Cell Epitopes ◽

B Cell Epitope ◽

Mouth Disease Virus ◽

Ifn Γ

Dendrimeric peptide constructs based on a lysine core that comprises both B- and T-cell epitopes of foot-and-mouth disease virus (FMDV) have proven a successful strategy for the development of FMD vaccines. Specifically, B2T dendrimers displaying two copies of the major type O FMDV antigenic B-cell epitope located on the virus capsid [VP1 (140–158)], covalently linked to a heterotypic T-cell epitope from either non-structural protein 3A [3A (21–35)] or 3D [3D (56–70)], named B2T-3A and B2T-3D, respectively, elicit high levels of neutralizing antibodies (nAbs) and IFN-γ-producing cells in pigs. To assess whether the inclusion and orientation of T-3A and T-3D T-cell epitopes in a single molecule could modulate immunogenicity, dendrimers with T epitopes juxtaposed in both possible orientations, i.e., constructs B2TT-3A3D and B2TT-3D3A, were made and tested in pigs. Both dendrimers elicited high nAbs titers that broadly neutralized type O FMDVs, although B2TT-3D3A did not respond to boosting, and induced lower IgGs titers, in particular IgG2, than B2TT-3A3D. Pigs immunized with B2, a control dendrimer displaying two B-cell epitope copies and no T-cell epitope, gave no nABs, confirming T-3A and T-3D as T helper epitopes. The T-3D peptide was found to be an immunodominant, as it produced more IFN-γ expressing cells than T-3A in the in vitro recall assay. Besides, in pigs immunized with the different dendrimeric peptides, CD4+ T-cells were the major subset contributing to IFN-γ expression upon in vitro recall, and depletion of CD4+ cells from PBMCs abolished the production of this cytokine. Most CD4+IFN-γ+ cells showed a memory (CD4+2E3−) and a multifunctional phenotype, as they expressed both IFN-γ and TNF-α, suggesting that the peptides induced a potent Th1 pro-inflammatory response. Furthermore, not only the presence, but also the orientation of T-cell epitopes influenced the T-cell response, as B2TT-3D3A and B2 groups had fewer cells expressing both cytokines. These results help understand how B2T-type dendrimers triggers T-cell populations, highlighting their potential as next-generation FMD vaccines.

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Vaccination With a FAT1-Derived B Cell Epitope Combined With Tumor-Specific B and T Cell Epitopes Elicits Additive Protection in Cancer Mouse Models

Frontiers in Oncology ◽

10.3389/fonc.2018.00481 ◽

2018 ◽

Vol 8 ◽

Author(s):

Alberto Grandi ◽

Laura Fantappiè ◽

Carmela Irene ◽

Silvia Valensin ◽

Michele Tomasi ◽

...

Keyword(s):

T Cell ◽

B Cell ◽

Mouse Models ◽

Cell Epitope ◽

T Cell Epitopes ◽

B Cell Epitope

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In Silico Identification and in Vitro Analysis of B and T-Cell Epitopes of the Black Turtle Bean (Phaseolus Vulgaris L.) Lectin

Cellular Physiology and Biochemistry ◽

10.1159/000493496 ◽

2018 ◽

Vol 49 (4) ◽

pp. 1600-1614 ◽

Cited By ~ 3

Author(s):

Shudong He ◽

Jinlong Zhao ◽

Walid Elfalleh ◽

Mohamed Jemaà ◽

Hanju Sun ◽

...

Keyword(s):

Amino Acids ◽

T Cell ◽

Phaseolus Vulgaris ◽

B Cell ◽

Cell Epitope ◽

T Cell Epitope ◽

T Cell Epitopes ◽

Phaseolus Vulgaris L ◽

B Cell Epitopes ◽

B Cell Epitope

Background/Aims: The incidence of lectin allergic disease is increasing in recent decades, and definitive treatment is still lacking. Identification of B and T-cell epitopes of allergen will be useful in understanding the allergen antibody responses as well as aiding in the development of new diagnostics and therapy regimens for lectin poisoning. In the current study, we mainly addressed these questions. Methods: Three-dimensional structure of the lectin from black turtle bean (Phaseolus vulgaris L.) was modeled using the structural template of Phytohemagglutinin from P. vulgaris (PHA-E, PDB ID: 3wcs.1.A) with high identity. The B and T-cell epitopes were screened and identified by immunoinformatics and subsequently validated by ELISA, lymphocyte proliferation and cytokine profile analyses. Results: Seven potential B-cell epitopes (B1 to B7) were identified by sequence and structure based methods, while three T-cell epitopes (T1 to T3) were identified by the predictions of binding score and inhibitory concentration. The epitope peptides were synthesized. Significant IgE binding capability was found in B-cell epitopes (B2, B5, B6 and B7) and T2 (a cryptic B-cell epitope). T1 and T2 induced significant lymphoproliferation, and the release of IL-4 and IL-5 cytokine confirmed the validity of T-cell epitope prediction. Abundant hydrophobic amino acids were found in B-cell epitope and T-cell epitope regions by amino acid analysis. Positively charged amino acids, such as His residue, might be more favored for B-cell epitope. Conclusion: The present approach can be applied for the identification of epitopes in novel allergen proteins and thus for designing diagnostics and therapies in lectin allergy.

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B Epitope Multiplicity and B/T Epitope Orientation Influence Immunogenicity of Foot-and-Mouth Disease Peptide Vaccines

Clinical and Developmental Immunology ◽

10.1155/2013/475960 ◽

2013 ◽

Vol 2013 ◽

pp. 1-9 ◽

Cited By ~ 13

Author(s):

Esther Blanco ◽

Carolina Cubillos ◽

Noelia Moreno ◽

Juan Bárcena ◽

Beatriz G. de la Torre ◽

...

Keyword(s):

T Cell ◽

B Cell ◽

Neutralizing Antibodies ◽

Cell Epitope ◽

Foot And Mouth Disease ◽

Mouth Disease ◽

T Cell Epitope ◽

T Cell Epitopes ◽

B Cell Epitope ◽

Foot And Mouth

Synthetic peptides incorporating protective B- and T-cell epitopes are candidates for new safer foot-and-mouth disease (FMD) vaccines. We have reported that dendrimeric peptides including four copies of a B-cell epitope (VP1 136 to 154) linked to a T-cell epitope (3A 21 to 35) of FMD virus (FMDV) elicit potent B- and T-cell specific responses and confer protection to viral challenge, while juxtaposition of these epitopes in a linear peptide induces less efficient responses. To assess the relevance of B-cell epitope multivalency, dendrimers bearing two (B2T) or four (B4T) copies of the B-cell epitope from type O FMDV (a widespread circulating serotype) were tested in CD1 mice and showed that multivalency is advantageous over simple B-T-epitope juxtaposition, resulting in efficient induction of neutralizing antibodies and optimal release of IFNγ. Interestingly, the bivalent B2T construction elicited similar or even better B- and T-cell specific responses than tetravalent B4T. In addition, the presence of the T-cell epitope and its orientation were shown to be critical for the immunogenicity of the linear juxtaposed monovalent peptides analyzed in parallel. Taken together, our results provide useful insights for a more accurate design of FMD subunit vaccines.

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Using Immunoinformatics to Design a mRNA Vaccine against the Spike Glycoprotein of SARS-CoV-2

ROMANIAN BIOTECHNOLOGICAL LETTERS ◽

10.25083/rbl/26.5/2901.2915 ◽

2021 ◽

Vol 26 (5) ◽

pp. 2901-2915

Author(s):

SHEREEN F. ELKHOLY ◽

Keyword(s):

T Cell ◽

B Cell ◽

T Lymphocyte ◽

Cell Epitope ◽

T Cell Epitopes ◽

Spike Glycoprotein ◽

Ifn Gamma ◽

Robust Immune Response ◽

B Cell Epitope ◽

Public Health Challenge

The rapid outbreak of the new coronavirus SARS-COV-2 has created a major public health challenge. Immunoinformatics tools had a clear effect in tracking the genetic sequence of the virus and monitoring mutations and design vaccines that are effective enough to produce antibodies. In our study, we resorted to the emerging discipline of immunoinformatics in order to design a multi-epitope mRNA vaccine against the spike glycoprotein of SARS-CoV-2. We screened the B cell and T cell epitopes of the Spike glycoprotein. we used ABC pred server to predict B cell epitope in the spike glycoprotein sequence and we used NetMHC-4.1 server to predict the T-cell epitope. Then we selected the B cell and T cell epitopes that fulfilled the antigenicity, non-toxicity, non-allergenicity, induction of both IL4 and IFN gamma. Finally, we designed multi-epitope mRNA Vaccine construct by linking 6 B lymphocytes epitopes (BL) with 6 cytotoxic T lymphocytes epitopes (CTL) together with helper T lymphocyte (HTL) epitope up-streamed by 5’ cap and down-streamed by poly A tail. The vaccine was found to be antigenic, non-toxic, non-allergenic, capable of generating a robust immune response. Based on these parameters, this design can be considered a promising choice for a vaccine against SARS-CoV-2.

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

Genome Medicine ◽

10.1186/s13073-021-00910-1 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Christof C. Smith ◽

Kelly S. Olsen ◽

Kaylee M. Gentry ◽

Maria Sambade ◽

Wolfgang Beck ◽

...

Keyword(s):

T Cell ◽

B Cell ◽

Cell Epitope ◽

T Cell Responses ◽

Sequence Conservation ◽

Conformational Space ◽

T Cell Epitope ◽

T Cell Epitopes ◽

Cell Responses ◽

B Cell Epitope

Abstract Background Early in the pandemic, we designed a SARS-CoV-2 peptide vaccine containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation. The rationale for this design was to drive both humoral and cellular immunity with high specificity while avoiding undesired effects such as antibody-dependent enhancement (ADE). Methods We explored the set of computationally predicted SARS-CoV-2 HLA-I and HLA-II ligands, examining protein source, concurrent human/murine coverage, and population coverage. Beyond MHC affinity, T cell vaccine candidates were further refined by predicted immunogenicity, sequence conservation, source protein abundance, and coverage of high frequency HLA alleles. B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering for surface accessibility, sequence conservation, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. Results From 58 initial candidates, three B cell epitope regions were identified. From 3730 (MHC-I) and 5045 (MHC-II) candidate ligands, 292 CD8+ and 284 CD4+ T cell epitopes were identified. By combining these B cell and T cell analyses, as well as a manufacturability heuristic, we proposed a set of 22 SARS-CoV-2 vaccine peptides for use in subsequent murine studies. We curated a dataset of ~ 1000 observed T cell epitopes from convalescent COVID-19 patients across eight studies, showing 8/15 recurrent epitope regions to overlap with at least one of our candidate peptides. Of the 22 candidate vaccine peptides, 16 (n = 10 T cell epitope optimized; n = 6 B cell epitope optimized) were manually selected to decrease their degree of sequence overlap and then synthesized. The immunogenicity of the synthesized vaccine peptides was validated using ELISpot and ELISA following murine vaccination. Strong T cell responses were observed in 7/10 T cell epitope optimized peptides following vaccination. Humoral responses were deficient, likely due to the unrestricted conformational space inhabited by linear vaccine peptides. Conclusions Overall, we find our selection process and vaccine formulation to be appropriate for identifying T cell epitopes and eliciting T cell responses against those epitopes. Further studies are needed to optimize prediction and induction of B cell responses, as well as study the protective capacity of predicted T and B cell epitopes.

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Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment

Pathogens ◽

10.3390/pathogens9050324 ◽

2020 ◽

Vol 9 (5) ◽

pp. 324 ◽

Cited By ~ 43

Author(s):

Takahiko Koyama ◽

Dilhan Weeraratne ◽

Jane L. Snowdon ◽

Laxmi Parida

Keyword(s):

Rna Polymerase ◽

B Cell ◽

Genetic Drift ◽

Vaccine Development ◽

Cell Epitope ◽

Spike Protein ◽

Immune Recognition ◽

T Cell Epitopes ◽

Antibody Treatment ◽

B Cell Epitope

New coronavirus (SARS-CoV-2) treatments and vaccines are under development to combat COVID-19. Several approaches are being used by scientists for investigation, including (1) various small molecule approaches targeting RNA polymerase, 3C-like protease, and RNA endonuclease; and (2) exploration of antibodies obtained from convalescent plasma from patients who have recovered from COVID-19. The coronavirus genome is highly prone to mutations that lead to genetic drift and escape from immune recognition; thus, it is imperative that sub-strains with different mutations are also accounted for during vaccine development. As the disease has grown to become a pandemic, B-cell and T-cell epitopes predicted from SARS coronavirus have been reported. Using the epitope information along with variants of the virus, we have found several variants which might cause drifts. Among such variants, 23403A>G variant (p.D614G) in spike protein B-cell epitope is observed frequently in European countries, such as the Netherlands, Switzerland, and France, but seldom observed in China.

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Allergen immunotherapy with the hypoallergenic B‐cell epitope‐based vaccine BM32 modifies IL‐10‐ and IL‐5‐secreting T cells

Allergy ◽

10.1111/all.13996 ◽

2019 ◽

Vol 75 (2) ◽

pp. 450-453 ◽

Cited By ~ 7

Author(s):

Michèle Myriam Rauber ◽

Christian Möbs ◽

Raffaela Campana ◽

Rainer Henning ◽

Manuel Schulze‐Dasbeck ◽

...

Keyword(s):

T Cells ◽

B Cell ◽

Allergen Immunotherapy ◽

Cell Epitope ◽

B Cell Epitope

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Repertoires of T cells directed against a large protein antigen, beta-galactosidase. II. Only certain T helper or T suppressor cells are relevant in particular regulatory interactions.

Journal of Experimental Medicine ◽

10.1084/jem.162.1.311 ◽

1985 ◽

Vol 162 (1) ◽

pp. 311-323 ◽

Cited By ~ 32

Author(s):

U Krzych ◽

A V Fowler ◽

E E Sercarz

Keyword(s):

T Cells ◽

B Cell ◽

Cell Epitope ◽

Suppressor Cells ◽

Amino Acid Residues ◽

T Helper ◽

Large Protein ◽

B Cell Epitope ◽

Beta Galactosidase

11 cyanogen bromide (CB) peptides, comprising 70% of the large protein, Escherichia coli beta-galactosidase (GZ), were studied for their ability to induce T suppressor (Ts) cells capable of strongly suppressing the in vitro anti-fluorescein (FITC) response to GZ-FITC. Only CB-2 (amino acid residues 3-92) and CB-3 (residues 93-187) were found to bear such Ts-inducing epitopes. In examining the specificity of T helper cell (Th) targets susceptible to CB-2 and CB-3-specific Ts, it appeared that only nearly Th targets could be suppressed. Thus, CB-10-primed Th were not suppressed by either Ts; even CB-3-primed Ts did not suppress CB-2-specific Th, although CB-2-specific Ts were effective. Furthermore, analysis of the suppression pattern revealed a hierarchical use of potential epitopes on native GZ in triggering functional regulatory T cells. A dominant Th epitope near the amino terminus of GZ tops a hierarchy of potential Th, most of which are never engaged. The dominant determinant seems to exist on the peptide CB-2-3 (residues 3-187), and presumably is destroyed by its cleavage at Met 92; the Th cells that it induces are suppressible by each of the Ts-inducing peptides. In the GZ system, where the native antigen is quite large, the interactions between Th and Ts are highly circumscribed. This may be attributable to the topology of antigen fragments produced during processing; any relevant fragment must bear at least a Ts- and Th-reactive determinant to permit intercellular regulation. A final implication of these results is that, not only does the existence of a Th-inducing determinant depend on its being an appropriate distance from a B cell epitope, but the existence of Ts-inducing determinants likewise depends on the existence of a neighboring Th-B cell association.

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In silico analysis suggests less effective MHC-II presentation of SARS-CoV-2 RBM peptides: Implication for neutralizing antibody responses

PLoS ONE ◽

10.1371/journal.pone.0246731 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0246731

Author(s):

Andrea Castro ◽

Kivilcim Ozturk ◽

Maurizio Zanetti ◽

Hannah Carter

Keyword(s):

T Cell ◽

B Cell ◽

Neutralizing Antibodies ◽

Cell Epitope ◽

Neutralizing Antibody ◽

Antibody Responses ◽

Binding Motif ◽

T Cell Epitopes ◽

Mhc Ii ◽

B Cell Epitope

SARS-CoV-2 antibodies develop within two weeks of infection, but wane relatively rapidly post-infection, raising concerns about whether antibody responses will provide protection upon re-exposure. Here we revisit T-B cooperation as a prerequisite for effective and durable neutralizing antibody responses centered on a mutationally constrained RBM B cell epitope. T-B cooperation requires co-processing of B and T cell epitopes by the same B cell and is subject to MHC-II restriction. We evaluated MHC-II constraints relevant to the neutralizing antibody response to a mutationally-constrained B cell epitope in the receptor binding motif (RBM) of the spike protein. Examining common MHC-II alleles, we found that peptides surrounding this key B cell epitope are predicted to bind poorly, suggesting a lack MHC-II support in T-B cooperation, impacting generation of high-potency neutralizing antibodies in the general population. Additionally, we found that multiple microbial peptides had potential for RBM cross-reactivity, supporting previous exposures as a possible source of T cell memory.

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