scholarly journals Characterization of Conserved and Promiscuous Human Rhinovirus CD4 T Cell Epitopes

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2294
Author(s):  
Marta Gomez-Perosanz ◽  
Tara Fiyouzi ◽  
Miguel Fernandez-Arquero ◽  
John Sidney ◽  
Alessandro Sette ◽  
...  
Keyword(s):  
T Cell ◽  
Respiratory Infections ◽  
Intracellular Cytokine Staining ◽  
Human Leukocyte ◽  
Human Rhinovirus ◽  
Cd4 T Cell ◽  
World Population ◽  
Intracellular Cytokine ◽  
T Cell Epitopes ◽  
Binding Assays

Human rhinovirus (RV) is the most common cause of upper respiratory infections and exacerbations of asthma. In this work, we selected 14 peptides (6 from RV A and 8 from RV C) encompassing potential CD4 T cell epitopes. Peptides were selected for being highly conserved in RV A and C serotypes and predicted to bind to multiple human leukocyte antigen class II (HLA II) molecules. We found positive T cell recall responses by interferon gamma (IFNγ)-ELISPOT assays to eight peptides, validating seven of them (three from RV A and four from RV C) as CD4 T cell epitopes through intracellular cytokine staining assays. Additionally, we verified their promiscuous binding to multiple HLA II molecules by quantitative binding assays. According to their experimental HLA II binding profile, the combination of all these seven epitopes could be recognized by >95% of the world population. We actually determined IFNγ responses to a pool encompassing these CD4 T cell epitopes by intracellular cytokine staining, finding positive responses in 29 out of 30 donors. The CD4 T cell epitopes identified in this study could be key to monitor RV infections and to develop peptide-based vaccines against most RV A and C serotypes.

scholarly journals Characterization of Conserved and Promiscuous Human Rhinovirus CD4 T Cell Epitopes

2021 ◽  
Author(s):  
Marta Gomez-Perosanz ◽  
Tara Fiyouzi ◽  
Miguel Fernandez-Arquero ◽  
John Sidney ◽  
Alessandro Sette ◽  
...  
Keyword(s):  
T Cell ◽  
Respiratory Infections ◽  
Intracellular Cytokine Staining ◽  
Human Rhinovirus ◽  
Cd4 T Cell ◽  
World Population ◽  
Intracellular Cytokine ◽  
T Cell Epitopes ◽  
Binding Assays

Human Rhinovirus (HRV) is the most common cause of upper respiratory infections and exacerbations of asthma. In this work, we selected 14 peptides (6 from HRV A and 8 from HRV C) encompassing potential CD4 T cell epitopes. Peptides were selected for being highly conserved in HRV A and C serotypes and predicted to bind to multiple HLA II molecules. We found positive T cell recall responses by IFNγ-ELISPOT assays to 8 peptides, validating 7 of them (3 from HRV A and 4 from HRV C) as CD4 T cell epitopes through intracellular cytokine staining assays. Additionally, we verified their promiscuous binding to multiple HLA II molecules by quantitative binding assays. According to their experimental HLA II binding profile, the combination of all these 7 epitopes could be presented and recognized by > 95 % of the world population. We actually determined IFNγ responses to a pool encompassing these CD4 T cell epitopes by intracellular cytokine staining, finding positive responses in 29 out of 30 donors. The CD4 T cell epitopes identified in this study could be key to monitor HRV infections and to develop peptide-based vaccines against most HRV A and C serotypes.

scholarly journals Lymphocytic Choriomeningitis Virus Infection Yields Overlapping CD4+ and CD8+ T-Cell Responses

2008 ◽  
Vol 82 (23) ◽  
pp. 11734-11741 ◽  
Author(s):  
Courtney Dow ◽  
Carla Oseroff ◽  
Bjoern Peters ◽  
Courtney Nance-Sotelo ◽  
John Sidney ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Intracellular Cytokine Staining ◽  
T Cell Responses ◽  
Lymphocytic Choriomeningitis ◽  
Lymphocytic Choriomeningitis Virus ◽  
T Cell Epitopes ◽  
Binding Assays ◽  
Cell Responses ◽  
Lymphocytic Choriomeningitis Virus Infection

ABSTRACT Activation of CD4+ T cells helps establish and sustain other immune responses. We have previously shown that responses against a broad set of nine CD4+ T-cell epitopes were present in the setting of lymphocytic choriomeningitis virus (LCMV) Armstrong infection in the context of H-2d. This is quite disparate to the H-2b setting, where only two epitopes have been identified. We were interested in determining whether a broad set of responses was unique to H-2d or whether additional CD4+ T-cell epitopes could be identified in the setting of the H-2b background. To pursue this question, we infected C57BL/6 mice with LCMV Armstrong and determined the repertoire of CD4+ T-cell responses using overlapping 15-mer peptides corresponding to the LCMV Armstrong sequence. We confirmed positive responses by intracellular cytokine staining and major histocompatibility complex (MHC)-peptide binding assays. A broad repertoire of responses was identified, consisting of six epitopes. These epitopes originate from the nucleoprotein (NP) and glycoprotein (GP). Out of the six newly identified CD4+ epitopes, four of them also stimulate CD8+ T cells in a statistically significant manner. Furthermore, we assessed these CD4+ T-cell responses during the memory phase of LCMV Armstrong infection and after infection with a chronic strain of LCMV and determined that a subset of the responses could be detected under these different conditions. This is the first example of a broad repertoire of shared epitopes between CD4+ and CD8+ T cells in the context of viral infection. These findings demonstrate that immunodominance is a complex phenomenon in the context of helper responses.

scholarly journals Design of Peptide Vaccine for COVID19: CD8+ and CD4+ T cell epitopes from SARS-CoV-2 open-reading-frame protein variants

2021 ◽  
Author(s):  
Simone Parn ◽  
Gabriel Jabbour ◽  
Vincent Nguyenkhoa ◽  
Sivanesan Dakshanamurthy
Keyword(s):  
T Cell ◽  
Vaccine Development ◽  
Human Life ◽  
Peptide Vaccine ◽  
T Cell Response ◽  
Cd4 T Cell ◽  
World Population ◽  
T Cell Epitopes ◽  
The World ◽  
Potential Vaccine

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has challenged public health at an unprecedented scale which has led to a dramatic loss of human life worldwide. To design a protective vaccine against SARS-CoV-2, it is necessary to understand which SARS-CoV-2 specific epitopes can elicit a T cell response and provide protection across a broad population. In this study, PLpro and RdRp, two immunogenic non-structural proteins from an immunodominant gene region ORF1ab, as well as ORF3a and ORF9b are identified as potential vaccine targets against SARS-CoV-2. To select top epitopes for vaccine design, we used various clinical properties, such as antigenicity, allergenicity, toxicity and IFN-y secretion. The analysis of CD8 and CD4 T cell epitopes revealed multiple potential vaccine constructs that cover a high percentage of the world population. We identified 8 immunogenic, antigenic, non-allergenic, non-toxic, stable and IFN-y inducing CD8 proteins for nsp3, 4 for nsp12, 11 for ORF3a and 3 for ORF9b that are common across four lineages of variants of concern: B.1.1.7, P.1, B.1.351 and B.1.617.2, which protect 98.12%, 87.08%, 96.07% and 63.8% of the world population, respectively. We also identified variant specific T cell epitopes that could be useful in targeting each variant strain separately. Including the prediction of mouse MHC affinity towards our top CD8 epitopes, our study revealed a total of 3 immunogenic, antigenic, non-allergenic, non-toxic, stable and IFN-y inducing CD8 epitopes overlapping with 6 antigenic, non-allergenic, non-toxic, stable and IFN-y inducing CD4 epitopes across all four variants of concern which can effectively be utilized in pre-clinical studies. The landscape of SARS-CoV-2 T cell epitopes that we identified can help lead SARS-CoV-2 vaccine development as well as epitope-based peptide vaccine research in the future.

Optimization of intracellular cytokine staining for the quantitation of antigen-specific CD4+ T cell responses in rhesus macaques

2004 ◽  
Vol 288 (1-2) ◽  
pp. 61-79 ◽  
Author(s):  
Marie-Claire Gauduin ◽  
Amitinder Kaur ◽  
Shabbir Ahmad ◽  
Tilahun Yilma ◽  
Jeffrey D. Lifson ◽  
...  
Keyword(s):  
T Cell ◽  
Rhesus Macaques ◽  
Intracellular Cytokine Staining ◽  
T Cell Responses ◽  
Cd4 T Cell ◽  
Intracellular Cytokine ◽  
Cell Responses

Analysis of the human cytomegalovirus pp65-directed T-cell response in healthy HLA-A2-positive individuals

2008 ◽  
Vol 389 (5) ◽  
Author(s):  
Juliane Schalich ◽  
Oresta Vytvytska ◽  
Wolfgang Zauner ◽  
Michael B. Fischer ◽  
Michael Buschle ◽  
...  
Keyword(s):  
T Cell ◽  
Human Cytomegalovirus ◽  
Mononuclear Cells ◽  
Intracellular Cytokine Staining ◽  
Human Leukocyte ◽  
Class Ii ◽  
T Cell Response ◽  
T Cell Epitopes ◽  
Peripheral Blood Mononuclear ◽  
Binding Data

AbstractHuman cytomegalovirus (HCMV) is contained by T-lymphocyte responses focused towards the major tegument protein pp65. To systematically identify T-cell epitopes, we applied the following strategy: 441 overlapping 15mer peptides spanning the entire HCMV pp65 antigen in 1-aa steps were screened in enzyme-linked immunospot (ELIspot) assays for interferon gamma (IFN-γ) secretion by peripheral blood mononuclear cells (PBMCs) from nine healthy HCMV-seropositive subjects expressing human leukocyte antigen (HLA)-A2. This analysis confirmed a number of previously known epitopes and revealed several new ones. A total of 26 epitopes were identified, including 14 HLA-A2, four HLA-B7, -B35, -B12 and -B44 restricted class I epitopes, six class II epitopes, and two epitopes of unknown restriction. Three novel HLA-A2 epitopes were confirmed using T2-cells, and one peptide for which only binding data had been published so far was verified. Two novel class II epitopes were confirmed by intracellular cytokine staining. Responses were usually oligoclonal against up to seven HLA-A2 epitopes, albeit with a few dominating epitopes. Clusters of overlapping epitopes (hot-spots) were identified. These and the newly identified T-cell epitopes may be of great value for epitope-based immunotherapeutic approaches, including peptide vaccines.

scholarly journals Computational assembly of a human Cytomegalovirus vaccine upon experimental epitope legacy

2019 ◽  
Vol 20 (S6) ◽  
Author(s):  
Monica J. Quinzo ◽  
Esther M. Lafuente ◽  
Pilar Zuluaga ◽  
Darren R. Flower ◽  
Pedro A. Reche
Keyword(s):  
T Cell ◽  
B Cell ◽  
Human Cytomegalovirus ◽  
Cd4 T Cell ◽  
World Population ◽  
T Cell Epitopes ◽  
Cell Component ◽  
Universal Vaccine ◽  
Cell Responses ◽  
Immunosuppressed Patients

Abstract Background Human Cytomegalovirus (HCMV) is a ubiquitous herpesvirus affecting approximately 90% of the world population. HCMV causes disease in immunologically naive and immunosuppressed patients. The prevention, diagnosis and therapy of HCMV infection are thus crucial to public health. The availability of effective prophylactic and therapeutic treatments remain a significant challenge and no vaccine is currently available. Here, we sought to define an epitope-based vaccine against HCMV, eliciting B and T cell responses, from experimentally defined HCMV-specific epitopes. Results We selected 398 and 790 experimentally validated HCMV-specific B and T cell epitopes, respectively, from available epitope resources and apply a knowledge-based approach in combination with immunoinformatic predictions to ensemble a universal vaccine against HCMV. The T cell component consists of 6 CD8 and 6 CD4 T cell epitopes that are conserved among HCMV strains. All CD8 T cell epitopes were reported to induce cytotoxic activity, are derived from early expressed genes and are predicted to provide population protection coverage over 97%. The CD4 T cell epitopes are derived from HCMV structural proteins and provide a population protection coverage over 92%. The B cell component consists of just 3 B cell epitopes from the ectodomain of glycoproteins L and H that are highly flexible and exposed to the solvent. Conclusions We have defined a multiantigenic epitope vaccine ensemble against the HCMV that should elicit T and B cell responses in the entire population. Importantly, although we arrived to this epitope ensemble with the help of computational predictions, the actual epitopes are not predicted but are known to be immunogenic.

scholarly journals West Nile Virus Vaccine Design by T Cell Epitope Selection: In Silico Analysis of Conservation, Functional Cross-Reactivity with the Human Genome, and Population Coverage

2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
Frances M. Waller ◽  
Pedro A. Reche ◽  
Darren R. Flower
Keyword(s):  
West Nile Virus ◽  
T Cell ◽  
Cell Epitope ◽  
Human Leukocyte ◽  
Medical Intervention ◽  
Cross Reactivity ◽  
World Population ◽  
T Cell Epitopes ◽  
West Nile ◽  
Multiple Sequence

West Nile Virus (WNV) causes a debilitating and life-threatening neurological disease in humans. Since its emergence in Africa 50 years ago, new strains of WNV and an expanding geographical distribution have increased public health concerns. There are no licensed therapeutics against WNV, limiting effective infection control. Vaccines represent the most efficacious and efficient medical intervention known. Epitope-based vaccines against WNV remain significantly underexploited. Here, we use a selection protocol to identify a set of conserved prevalidated immunogenic T cell epitopes comprising a putative WNV vaccine. Experimentally validated immunogenic WNV epitopes and WNV sequences were retrieved from the IEDB and West Nile Virus Variation Database. Clustering and multiple sequence alignment identified a smaller subset of representative sequences. Protein variability analysis identified evolutionarily conserved sequences, which were used to select a diverse set of immunogenic candidate T cell epitopes. Cross-reactivity and human leukocyte antigen-binding affinities were assessed to eliminate unsuitable epitope candidates. Population protection coverage (PPC) quantified individual epitopes and epitope combinations against the world population. 3 CD8+ T cell epitopes (ITYTDVLRY, TLARGFPFV, and SYHDRRWCF) and 1 CD4+ epitope (VTVNPFVSVATANAKVLI) were selected as a putative WNV vaccine, with an estimated PPC of 97.14%.

scholarly journals Immunoinformatics Analysis of SARS-CoV-2 ORF1ab Polyproteins to Identify Promiscuous and Highly Conserved T-Cell Epitopes to Formulate Vaccine for Indonesia and the World Population

Vaccines ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 1459
Author(s):  
Marsia Gustiananda ◽  
Bobby Prabowo Sulistyo ◽  
David Agustriawan ◽  
Sita Andarini
Keyword(s):  
T Cell ◽  
Cell Epitope ◽  
Docking Simulation ◽  
Human Leukocyte ◽  
In Vitro Study ◽  
Hla Class I ◽  
World Population ◽  
T Cell Epitopes ◽  
Docking Simulations

SARS-CoV-2 and its variants caused the COVID-19 pandemic. Vaccines that target conserved regions of SARS-CoV-2 and stimulate protective T-cell responses are important for reducing symptoms and limiting the infection. Seven cytotoxic (CTL) and five helper T-cells (HTL) epitopes from ORF1ab were identified using NetCTLpan and NetMHCIIpan algorithms, respectively. These epitopes were generated from ORF1ab regions that are evolutionary stable as reflected by zero Shannon’s entropy and are presented by 56 human leukocyte antigen (HLA) Class I and 22 HLA Class II, ensuring good coverage for the Indonesian and world population. Having fulfilled other criteria such as immunogenicity, IFNγ inducing ability, and non-homology to human and microbiome peptides, the epitopes were assembled into a vaccine construct (VC) together with β-defensin as adjuvant and appropriate linkers. The VC was shown to have good physicochemical characteristics and capability of inducing CTL as well as HTL responses, which stem from the engagement of the vaccine with toll-like receptor 4 (TLR4) as revealed by docking simulations. The most promiscuous peptide 899WSMATYYLF907 was shown via docking simulation to interact well with HLA-A*24:07, the most predominant allele in Indonesia. The data presented here will contribute to the in vitro study of T-cell epitope mapping and vaccine design in Indonesia.

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