A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach

Emerging infectious diseases (EIDs) caused by viruses are increasing in frequency, causing a high disease burden and mortality world-wide. The COVID-19 pandemic caused by the novel SARS-like coronavirus (SARS-CoV-2) underscores the need to innovate and accelerate the development of effective vaccination strategies against EIDs. Human leukocyte antigen (HLA) molecules play a central role in the immune system by determining the peptide repertoire displayed to the T-cell compartment. Genetic polymorphisms of the HLA system thus confer a strong variability in vaccine-induced immune responses and may complicate the selection of vaccine candidates, because the distribution and frequencies of HLA alleles are highly variable among different ethnic groups. Herein, we build on the emerging paradigm of rational epitope-based vaccine design, by describing an immunoinformatics tool (Predivac-3.0) for proteome-wide T-cell epitope discovery that accounts for ethnic-level variations in immune responsiveness. Predivac-3.0 implements both CD8+ and CD4+ T-cell epitope predictions based on HLA allele frequencies retrieved from the Allele Frequency Net Database. The tool was thoroughly assessed, proving comparable performances (AUC ~0.9) against four state-of-the-art pan-specific immunoinformatics methods capable of population-level analysis (NetMHCPan-4.0, Pickpocket, PSSMHCPan and SMM), as well as a strong accuracy on proteome-wide T-cell epitope predictions for HIV-specific immune responses in the Japanese population. The utility of the method was investigated for the COVID-19 pandemic, by performing in silico T-cell epitope mapping of the SARS-CoV-2 spike glycoprotein according to the ethnic context of the countries where the ChAdOx1 vaccine is currently initiating phase III clinical trials. Potentially immunodominant CD8+ and CD4+ T-cell epitopes and population coverages were predicted for each population (the Epitope Discovery mode), along with optimized sets of broadly recognized (promiscuous) T-cell epitopes maximizing coverage in the target populations (the Epitope Optimization mode). Population-specific epitope-rich regions (T-cell epitope clusters) were further predicted in protein antigens based on combined criteria of epitope density and population coverage. Overall, we conclude that Predivac-3.0 holds potential to contribute in the understanding of ethnic-level variations of vaccine-induced immune responsiveness and to guide the development of epitope-based next-generation vaccines against emerging pathogens, whose geographic distributions and populations in need of vaccinations are often well-defined for regional epidemics.

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T cell epitope mapping identifies reactive CD4 T cell epitopes of ixekizumab, but not secukinumab

Journal of the American Academy of Dermatology ◽

10.1016/j.jaad.2019.10.108 ◽

2019 ◽

Vol 81 (4) ◽

pp. AB439

Keyword(s):

T Cell ◽

Epitope Mapping ◽

Cell Epitope ◽

Cd4 T Cell ◽

T Cell Epitope ◽

T Cell Epitopes

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A systematic, unbiased mapping of CD8+ and CD4+ T cell epitopes in Yellow Fever vaccinees

10.1101/2020.03.28.012468 ◽

2020 ◽

Cited By ~ 1

Author(s):

Anette Stryhn ◽

Michael Kongsgaard ◽

Michael Rasmussen ◽

Mikkel Nors Harndahl ◽

Thomas Østerbye ◽

...

Keyword(s):

T Cell ◽

Yellow Fever ◽

Cell Epitope ◽

T Cell Responses ◽

Hla Class I ◽

Class I ◽

T Cell Epitope ◽

T Cell Epitopes ◽

Cell Responses ◽

Epitope Discovery

1.AbstractExamining CD8+ and CD4+ T cell responses after primary Yellow Fever vaccination in a cohort of 210 volunteers, we have identified and tetramer-validated 92 CD8+ and 50 CD4+ T cell epitopes, many inducing strong and prevalent (i.e. immunodominant) T cell responses. Restricted by 40 and 14 HLA-class I and II allotypes, respectively, these responses have wide population coverage and might be of considerable academic, diagnostic and therapeutic interest. The broad coverage of epitopes and HLA overcame the otherwise confounding effects of HLA diversity and non-HLA background providing the first evidence of T cell immunodomination in humans. Also, double-staining of CD4+ T cells with tetramers representing the same HLA-binding core, albeit with different flanking regions, demonstrated an extensive diversification of the specificities of many CD4+ T cell responses. We suggest that this could reduce the risk of pathogen escape, and that multi-tetramer staining is required to reveal the true magnitude and diversity of CD4+ T cell responses. Our T cell epitope discovery approach uses a combination of 1) overlapping peptides representing the entire Yellow Fever virus proteome to search for peptides containing CD4+ and/or CD8+ T cell epitopes, 2) predictors of peptide-HLA binding to suggest epitopes and their restricting HLA allotypes, 3) generation of peptide-HLA tetramers to identify T cell epitopes, and 4) analysis of ex vivo T cell responses to validate the same. This approach is systematic, exhaustive, and can be done in any individual of any HLA haplotype. It is all-inclusive in the sense that it includes all protein antigens and peptide epitopes, and encompasses both CD4+ and CD8+ T cell epitopes. It is efficient and, importantly, reduces the false discovery rate. The unbiased nature of the T cell epitope discovery approach presented here should support the refinement of future peptide-HLA class I and II predictors and tetramer technologies, which eventually should cover all HLA class I and II isotypes. We believe that future investigations of emerging pathogens (e.g. SARS-CoV-2) should include population-wide T cell epitope discovery using blood samples from patients, convalescents and/or long-term survivors, who might all hold important information on T cell epitopes and responses.

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T-cell epitope vaccine design by immunoinformatics

Open Biology ◽

10.1098/rsob.120139 ◽

2013 ◽

Vol 3 (1) ◽

pp. 120139 ◽

Cited By ~ 182

Author(s):

Atanas Patronov ◽

Irini Doytchinova

Keyword(s):

T Cell ◽

Immune Responses ◽

Molecular Level ◽

Active Agent ◽

Cell Epitope ◽

Antigen Recognition ◽

T Cell Epitope ◽

T Cell Epitopes ◽

Peptide Vaccines ◽

Foreign Antigen

Vaccination is generally considered to be the most effective method of preventing infectious diseases. All vaccinations work by presenting a foreign antigen to the immune system in order to evoke an immune response. The active agent of a vaccine may be intact but inactivated (‘attenuated’) forms of the causative pathogens (bacteria or viruses), or purified components of the pathogen that have been found to be highly immunogenic. The increased understanding of antigen recognition at molecular level has resulted in the development of rationally designed peptide vaccines. The concept of peptide vaccines is based on identification and chemical synthesis of B-cell and T-cell epitopes which are immunodominant and can induce specific immune responses. The accelerating growth of bioinformatics techniques and applications along with the substantial amount of experimental data has given rise to a new field, called immunoinformatics. Immunoinformatics is a branch of bioinformatics dealing with in silico analysis and modelling of immunological data and problems. Different sequence- and structure-based immunoinformatics methods are reviewed in the paper.

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CD4+ T Cell Epitope Discovery and Rational Vaccine Design

Archivum Immunologiae et Therapiae Experimentalis ◽

10.1007/s00005-010-0067-0 ◽

2010 ◽

Vol 58 (2) ◽

pp. 121-130 ◽

Cited By ~ 42

Author(s):

Daniela Santoro Rosa ◽

Susan Pereira Ribeiro ◽

Edecio Cunha-Neto

Keyword(s):

T Cell ◽

Cell Epitope ◽

Vaccine Design ◽

Cd4 T Cell ◽

T Cell Epitope ◽

Rational Vaccine Design ◽

Epitope Discovery

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Identification of novel T-cell epitopes on infectious bronchitis virus N protein and development of a multi-epitope vaccine

Journal of Virology ◽

10.1128/jvi.00667-21 ◽

2021 ◽

Author(s):

Yifeng Qin ◽

Kaihang Tu ◽

Qingyuan Teng ◽

Delan Feng ◽

Ye Zhao ◽

...

Keyword(s):

T Cell ◽

Immune Responses ◽

Vaccine Candidate ◽

Intracellular Cytokine Staining ◽

Cell Epitope ◽

T Cell Epitope ◽

T Cell Epitopes ◽

Epitope Vaccine ◽

N Protein ◽

Infectious Bronchitis

Cellular immune responses play a key role in the control of viral infection. The nucleocapsid (N) protein of infectious bronchitis virus (IBV) is a major immunogenic protein that can induce protective immunity. To screen for potential T-cell epitopes on IBV N protein, forty overlapping peptides covering the entirety of the N protein were designed and synthesized. Four T-cell epitope peptides were identified by IFN-γ ELISpot, intracellular cytokine staining, and CFSE lymphocyte proliferation assays; among them, three peptides (N 211–230 , N 271–290 , and N 381–400 ) were CTL epitopes, and one peptide (N 261–280 ) was a dual-specific T-cell epitope, which can be recognized by both CD8 + and CD4 + T cells. Multi-epitope gene transcription cassettes comprising four neutralizing epitope domains and four T-cell epitope peptides were synthesized and inserted into the genome of Newcastle disease virus strain La Sota between the P and M genes. Recombinant IBV multi-epitope vaccine candidate rLa Sota/SBNT was generated via reverse genetics, and its immune protection efficacy was evaluated in specific-pathogen-free chickens. Our results show that rLa Sota/SBNT induced IBV-specific neutralizing antibody and T-cell responses and provided significant protection against homologous and heterologous IBV challenge. Thus, the T-cell epitope peptides identified in this study could be good candidates for IBV vaccine development, and recombinant Newcastle disease virus expressing IBV multi-epitope genes represents a safe and effective vaccine candidate for controlling infectious bronchitis. IMPORTANCE T-cell-mediated immune responses are critical for the elimination of IBV-infected cells. To screen conserved T-cell epitopes in the IBV N protein, forty overlapping peptides covering the entirety of the N protein were designed and synthesized. By combining IFN-γ ELISpot, intracellular cytokine staining, and CFSE lymphocyte proliferation assays, we identified three CTL epitopes and one dual-specific T-cell epitope. The value of T-cell epitope peptides identified in the N protein was further verified by the design of an IBV multi-epitope vaccine. Results show that IBV multi-epitope vaccine candidate rLa Sota/SBNT provided cross protection against challenges with a QX-like or a TW-like IBV strain. So T-cell-mediated immune responses play an important role in the control of viral infection and conserved T-cell epitopes serve as promising candidates for use in multi-epitope vaccine construction. Our results provide a new perspective for the development of a safer and more effective IBV vaccine.

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Cytokine patterns of newly identified HEV-specific CD4 T cell epitope

10.1055/s-0039-3402257 ◽

2020 ◽

Author(s):

B Csernalabics ◽

M Smits ◽

K Zoldan ◽

M Panning ◽

C Neumann-Haefelin ◽

...

Keyword(s):

T Cell ◽

Cell Epitope ◽

Cd4 T Cell ◽

T Cell Epitope

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A novel CD4 T-cell epitope described from one of the cervical cancer patients vaccinated with HPV 16 or 18 E7-pulsed dendritic cells

Cancer Immunology Immunotherapy ◽

10.1007/s00262-008-0617-z ◽

2008 ◽

Vol 58 (2) ◽

pp. 309-309

Author(s):

Xuelian Wang ◽

Alessandro D. Santin ◽

Stefania Bellone ◽

Sushil Gupta ◽

Mayumi Nakagawa

Keyword(s):

Cervical Cancer ◽

Dendritic Cells ◽

T Cell ◽

Cancer Patients ◽

Cell Epitope ◽

Cd4 T Cell ◽

T Cell Epitope ◽

Hpv 16

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Mining the capacity of human-associated microorganisms to trigger rheumatoid arthritis—A systematic immunoinformatics analysis of T cell epitopes

PLoS ONE ◽

10.1371/journal.pone.0253918 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0253918

Author(s):

Jelena Repac ◽

Marija Mandić ◽

Tanja Lunić ◽

Bojan Božić ◽

Biljana Božić Nedeljković

Keyword(s):

Rheumatoid Arthritis ◽

T Cell ◽

De Novo ◽

Molecular Mimicry ◽

Sequence Similarity ◽

Cell Epitope ◽

Homology Search ◽

T Cell Epitope ◽

T Cell Epitopes ◽

Painful Condition

Autoimmune diseases, often triggered by infection, affect ~5% of the worldwide population. Rheumatoid Arthritis (RA)–a painful condition characterized by the chronic inflammation of joints—comprises up to 20% of known autoimmune pathologies, with the tendency of increasing prevalence. Molecular mimicry is recognized as the leading mechanism underlying infection-mediated autoimmunity, which assumes sequence similarity between microbial and self-peptides driving the activation of autoreactive lymphocytes. T lymphocytes are leading immune cells in the RA-development. Therefore, deeper understanding of the capacity of microorganisms (both pathogens and commensals) to trigger autoreactive T cells is needed, calling for more systematic approaches. In the present study, we address this problem through a comprehensive immunoinformatics analysis of experimentally determined RA-related T cell epitopes against the proteomes of Bacteria, Fungi, and Viruses, to identify the scope of organisms providing homologous antigenic peptide determinants. By this, initial homology screening was complemented with de novo T cell epitope prediction and another round of homology search, to enable: i) the confirmation of homologous microbial peptides as T cell epitopes based on the predicted binding affinity to RA-related HLA polymorphisms; ii) sequence similarity inference for top de novo T cell epitope predictions to the RA-related autoantigens to reveal the robustness of RA-triggering capacity for identified (micro/myco)organisms. Our study reveals a much larger repertoire of candidate RA-triggering organisms, than previously recognized, providing insights into the underestimated role of Fungi in autoimmunity and the possibility of a more direct involvement of bacterial commensals in RA-pathology. Finally, our study pinpoints Endoplasmic reticulum chaperone BiP as the most potent (most likely mimicked) RA-related autoantigen, opening an avenue for identifying the most potent autoantigens in a variety of different autoimmune pathologies, with possible implications in the design of next-generation therapeutics aiming to induce self-tolerance by affecting highly reactive autoantigens.

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