scholarly journals Improved prediction of Bovine Leucocyte Antigens (BoLA) presented ligands by use of MS eluted ligands and in-vitro binding data; impact for the identification T cell epitopes

2017 ◽  
Author(s):  
Morten Nielsen ◽  
Tim Connelley ◽  
Nicola Ternette
Keyword(s):  
T Cell ◽  
Attractive Alternative ◽  
Binding Motif ◽  
T Cell Epitopes ◽  
Mhc I ◽  
Binding Data ◽  
Vitro Binding ◽  
The Cost ◽  
Leucocyte Antigens

AbstractPeptide binding to MHC class I molecules is the single most selective step in antigen presentation and the strongest single correlate to peptide cellular immunogenicity. The cost of experimentally characterizing the rules of peptide presentation for a given MHC-I molecule is extensive, and predictors of peptide-MHC interactions constitute an attractive alternative.Recently, an increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is in general challenging due to the poly-specificity nature of the data. We here outline a general pipeline for dealing with this challenge, and accurately annotate ligands to the relevant MHC-I molecule they were eluted from by use of GibbsClustering and binding motif information inferred from in-silico models. We illustrate the approach here in the context of MHCI molecules (BoLA) of cattle. Next, we demonstrate how such annotated BoLA MS ligand data can readily be integrated with in-vitro binding affinity data in a prediction model with very high and unprecedented performance for identification of BoLA-I restricted T cell epitopes.The approach has here been applied to the BoLA-I system, but the pipeline is readily applicable to MHC systems in other species.

scholarly journals Immuno-proteomic interrogation of dengue infection reveals novel HLA haplotype-specific MHC-I antigens

2018 ◽  
Author(s):  
Kavya Swaminathan ◽  
Niclas Olsson ◽  
Peder J. Lund ◽  
Caleb D. Marceau ◽  
Lisa E. Wagar ◽  
...  
Keyword(s):  
T Cell ◽  
Cell Biology ◽  
Dengue Infection ◽  
Denv Infection ◽  
Peptide Ligands ◽  
T Cell Epitopes ◽  
Mhc I ◽  
Proteomics Approach ◽  
Mhc Ligands

AbstractBroadly effective vaccines against dengue virus (DENV) infection have remained elusive, despite rising infection rates in the developing world. Infection-specific peptide ligands presented on Major Histocompatibility Complexes (MHC) open new avenues for developing T-cell-based interventions. Past efforts towards mapping viral MHC epitopes were based on computational predictions that only partially reflected actual antigen presentation. To empirically identify DENV-specific MHC ligands, we developed an immuno-proteomics approach for interrogating DENV- and self-derived MHC ligands from infected B-lymphocytes. Here, we report four fundamental findings: First, over 700 infection-specific MHC-ligands reflected host cellular responses to DENV that were not apparent from the proteome. Second, we report 121 viral MHC-I ligands (108 novel) which clustered into discrete hotspots across the DENV polyprotein, some of which spanned DENV polyprotein components, described here as MHC ligands for the first time. Third, we found DENV ligands which were distinctly presented by MHC alleles previously associated with either high or low anti-DENV response. Fourth, we demonstrate that while our in vitro assay only overlapped with a small fraction of previously described DENV T-cell epitopes, several novel MHC ligands identified here were recognized by T-cells from DENV-infected patients despite having low binding affinities. Together, these discoveries suggest that virus and host-derived MHC ligands have under-exploited potential for describing the cell biology of DENV infection, and as candidates for designing effective DENV vaccines.

scholarly journals SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8+ T cell responses

2021 ◽  
Vol 6 (57) ◽  
pp. eabg6461
Author(s):  
Benedikt Agerer ◽  
Maximilian Koblischke ◽  
Venugopal Gudipati ◽  
Luis Fernando Montaño-Gutierrez ◽  
Mark Smyth ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Ex Vivo ◽  
Point Mutations ◽  
Transcriptional Response ◽  
T Cell Epitopes ◽  
Mhc I ◽  
Vitro Assay ◽  
Cell Immunity

CD8+ T cell immunity to SARS-CoV-2 has been implicated in COVID-19 severity and virus control. Here, we identified nonsynonymous mutations in MHC-I-restricted CD8+ T cell epitopes after deep sequencing of 747 SARS-CoV-2 virus isolates. Mutant peptides exhibited diminished or abrogated MHC-I binding in a cell-free in vitro assay. Reduced MHC-I binding of mutant peptides was associated with decreased proliferation, IFN-γ production and cytotoxic activity of CD8+ T cells isolated from HLA-matched COVID-19 patients. Single cell RNA sequencing of ex vivo expanded, tetramer-sorted CD8+ T cells from COVID-19 patients further revealed qualitative differences in the transcriptional response to mutant peptides. Our findings highlight the capacity of SARS-CoV-2 to subvert CD8+ T cell surveillance through point mutations in MHC-I-restricted viral epitopes.

Self-Peptide Recognition of Posterior Eye Segment Epitopes Mediated By Allogeneic T Cells in Patients Undergoing Allogeneic Hematopoietic Cell Transplantation

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1173-1173
Author(s):  
Nora Mirza ◽  
Manfred Zierhut ◽  
Andreas Korn ◽  
Antje Bornemann ◽  
Christoph Simon ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
T Cell Epitopes ◽  
Healthy Individuals ◽  
Cell Reactivity ◽  
Mhc I ◽  
Mhc Ii ◽  
T Cell Reactivity ◽  
Self Antigens

Abstract Graft versus Host Disease (GvHD) is the major complication of allogeneic hematopoetic cell transplantation (HCT). It mostly affects the gastrointestinal tract, skin or liver, but may also involve the central nervous system (CNS). Although GvHD is believed to be mainly mediated by T cells recognizing HLA mismatches or minor histocompatibility antigens (MHC-restricted peptides differing in single amino acids based on protein sequence variants between donor and recipient due to genetic differences), limited evidence is known about the exact MHC-restricted T cell epitopes recognized on recipient cells. In this study, we evaluated the clinical manifestation of GvHD in the posterior eye segment (PS) as part of the CNS and characterized self-antigens mediating reactivity of allogeneic T cells. The first patient group comprised 6 individuals (3 women and 3 men, median age 40 years, range 20-58 years) with diseases of the PS after HCT. Diseases were ALL (n=4), AML (n=1) and MPS (n=1). 8 transplantations (1-2 per patient) were performed using grafts from matched related (MRD, n=1), matched unrelated (MUD, n=4), mismatched unrelated (MMUD, n=2) or haploidentical (n=1) donors. The second group included 22 patients (7 women and 15 men, median age 55 years, range 29-69 years) irrespective of ocular symptoms recruited before HCT. Diseases were AML (n=7), CML (n=1), MDS (n=4), MPS (n=5), multiple myeloma (n=1) and lymphoma (n=4). All patients received grafts from HLA-identical donors (MRD n=7, MUD n=15). GvHD prophylaxis was performed using standard protocols. Peripheral blood mononuclear cells (PBMC) and DNA were isolated from blood samples. Autologous cell samples were blood samples before or oral mucosa after HCT. Allogeneic cells were obtained from patients with complete donor chimerism. DNA sequencing was performed to identify donor-recipient single nucleotide polymorphisms (SNP). Retina specific candidate epitopes derived from the retinal guanylate cyclase 2D (GUCY2D), the retinoid binding protein (RBP) and the guanylate cyclase activating proteins A1 und B1 (GUCA1A/GUCA1B) were predicted based on known SNP and individual protein sequences using the database EpiToolKit. PBMC were prestimulated with both wildtype and SNP peptides. T cell reactivity was determined in ELISpot and intracellular cytokine staining. Moreover, T cells from 5 family donors were evaluated. All epitopes were evaluated in at least 8 healthy individuals carrying the respective HLA-subtype. Immunogenicity of MHC-I restricted candidate epitopes was determined in in vitro priming. PS diagnoses were optical atrophy (n=2), in 1 case combined with a selective dysfunction of the cones, optic neuritis (n=2), anemic retinopathy (n=1) and VZV retinitis (n=1). In two of these patients (one with selective cone dystrophy, the other with VZV retinitis) antigen specific T cells against MHC-II restricted GUCY2D epitopes could be detected 24 and 40 months after HCT. DNA sequencing did not reveal a SNP indicating recognition of self-antigens. In 6/22 patients without PS symptoms, retina-specific T cells could be detected, here directed against MHC-II restricted epitopes derived from GUCA1A (n=3), GUCA1B (n=3) and GUCY2D (n=3) between 4 and 14 months after HCT. After stimulation with the variant peptide, no T cell reactivity occurred, confirming that the observed responses were sequence specific. T cell responses tended to increase over time but could disappear at certain time points. Again, no SNP could be observed. Hence, T cell reactivity was directed against self-epitopes. Transplantation of retina-antigen specific cells and cross-reactivity against naturally occurring epitopes were excluded since no reactivity could be detected in donor samples and healthy individuals. In in vitro priming experiments, 36/55 of MHC-I restricted peptides could be confirmed as T cell epitopes. Thus, GvHD manifestations of the retina can be detected in patients after allogeneic HCT and can be mediated by antigen-specific T cells. Development of PS GvHD may be triggered by viral infections and should be considered in case of atypical ophthalmologic findings. The antigens recognized hereby can be self-antigens and do not need to be based on genetic differences between donor and recipient. In summary, recognition of self-antigens by allogeneic T cells represents a novel pathomechanism of graft-host-interaction in patients undergoing allogeneic HCT. Disclosures No relevant conflicts of interest to declare.

scholarly journals In silico design and in vitro expression of novel multiepitope DNA constructs based on HIV-1 proteins and Hsp70 T-cell epitopes

2021 ◽  
Author(s):  
Elahe Akbari ◽  
Kimia Kardani ◽  
Ali Namvar ◽  
Soheila Ajdary ◽  
Esmat Mirabzadeh Ardakani ◽  
...  
Keyword(s):  
T Cell ◽  
In Silico ◽  
T Cell Epitopes ◽  
In Vitro Expression ◽  
In Silico Design ◽  
Hiv 1

scholarly journals Identification of Promiscuous African Swine Fever Virus T-Cell Determinants Using a Multiple Technical Approach

Vaccines ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 29
Author(s):  
Laia Bosch-Camós ◽  
Elisabet López ◽  
María Jesús Navas ◽  
Sonia Pina-Pedrero ◽  
Francesc Accensi ◽  
...  
Keyword(s):  
T Cell ◽  
Mononuclear Cells ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Cd8 T Cell ◽  
Protective Role ◽  
Full Length ◽  
T Cell Epitopes ◽  
Peripheral Blood Mononuclear

The development of subunit vaccines against African swine fever (ASF) is mainly hindered by the lack of knowledge regarding the specific ASF virus (ASFV) antigens involved in protection. As a good example, the identity of ASFV-specific CD8+ T-cell determinants remains largely unknown, despite their protective role being established a long time ago. Aiming to identify them, we implemented the IFNγ ELISpot as readout assay, using as effector cells peripheral blood mononuclear cells (PBMCs) from pigs surviving experimental challenge with Georgia2007/1. As stimuli for the ELISpot, ASFV-specific peptides or full-length proteins identified by three complementary strategies were used. In silico prediction of specific CD8+ T-cell epitopes allowed identifying a 19-mer peptide from MGF100-1L, as frequently recognized by surviving pigs. Complementarily, the repertoire of SLA I-bound peptides identified in ASFV-infected porcine alveolar macrophages (PAMs), allowed the characterization of five additional SLA I-restricted ASFV-specific epitopes. Finally, in vitro stimulation studies using fibroblasts transfected with plasmids encoding full-length ASFV proteins, led to the identification of MGF505-7R, A238L and MGF100-1L as promiscuously recognized antigens. Interestingly, each one of these proteins contain individual peptides recognized by surviving pigs. Identification of the same ASFV determinants by means of such different approaches reinforce the results presented here.

Human Cytotoxic T Cell Epitopes in HPV 11: Relationships between Allele-Specific Motifs, HLA Binding, and Stimulation in Vitro

1994 ◽  
pp. 227-232
Author(s):  
Huw Davies ◽  
Ian Tarpey ◽  
Simon Stacey ◽  
Julian Hickling ◽  
Jennifer Bartholomew ◽  
...  
Keyword(s):  
T Cell ◽  
Cytotoxic T Cell ◽  
T Cell Epitopes ◽  
Allele Specific ◽  
Hla Binding

scholarly journals Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved?

2018 ◽  
Author(s):  
Zheng-Rong Tiger Li ◽  
Veronika I. Zarnitsyna ◽  
Anice C. Lowen ◽  
Daniel Weissman ◽  
Katia Koelle ◽  
...  
Keyword(s):  
T Cell ◽  
Influenza A Virus ◽  
Influenza A ◽  
Cd8 T Cell ◽  
Influenza Vaccines ◽  
T Cell Epitopes ◽  
Word Count ◽  
Mhc I ◽  
Escape Variant ◽  
Replicative Fitness

AbstractThe high-degree conservation of CD8 T cell epitopes of influenza A virus (IAV) may allow T cell-inducing vaccines effective across different strains and subtypes. This conservation is not fully explained by functional constraint, since additional mutation(s) can compensate the replicative fitness loss of IAV escape-variant. Here, we propose three additional mechanisms that contribute to the conservation of CD8 T cell epitopes of IAV. First, influenza-specific CD8 T cells may protect predominantly against severe pathology rather than infection and may only have a modest effect on transmission. Second, polymorphism of human MHC-I gene restricts the advantage of an escape-variant to only a small fraction of human population, who carry the relevant MHC-I alleles. Finally, infection with CD8 T cell-escapevariants may result in compensatory increase in the responses to other epitopes of IAV. A combination of population genetics and epidemiological models is used to examine how the interplay between these mechanisms affects the rate of invasion of IAV escape-variants. We conclude that the invasion of an escape-variant will be very slow with a timescale of decades or longer, even if the escape-variant does not have a replicative fitness loss. Our results suggest T cell-inducing vaccines may not engender the rapid evolution of IAV and serve as a foundation for future modeling works on the long-term effectiveness and impacts of T cell-inducing influenza vaccines. (Word count: 221)ImportanceUniversal influenza vaccines against the conserved epitopes of influenza A virus have been proposed to minimize the burden of seasonal outbreaks and prepare for the pandemics. However, it is not clear to which extent the T cell-inducing vaccines will select for viruses that escape the T cell responses. Our mathematical models suggest how the nature of CD8 T cell protection contributes to the conservation of the CD8 T cell epitopes of influenza A virus. Also, it points out the essential biological parameters and questions that need addressing by future experimental works. (Word count: 91)

scholarly journals Anti-CD20 therapy depletes activated myelin-specific CD8+T cells in multiple sclerosis

2019 ◽  
Vol 116 (51) ◽  
pp. 25800-25807 ◽  
Author(s):  
Joseph J. Sabatino ◽  
Michael R. Wilson ◽  
Peter A. Calabresi ◽  
Stephen L. Hauser ◽  
Jonathan P. Schneck ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
T Cells ◽  
T Cell ◽  
Ex Vivo ◽  
Antibody Therapy ◽  
Myelin Proteins ◽  
T Cell Epitopes ◽  
Control Subjects ◽  
Anti Cd20

CD8+T cells are believed to play an important role in multiple sclerosis (MS), yet their role in MS pathogenesis remains poorly defined. Although myelin proteins are considered potential autoantigenic targets, prior studies of myelin-reactive CD8+T cells in MS have relied on in vitro stimulation, thereby limiting accurate measurement of their ex vivo precursor frequencies and phenotypes. Peptide:MHC I tetramers were used to identify and validate 5 myelin CD8+T cell epitopes, including 2 newly described determinants in humans. The validated tetramers were used to measure the ex vivo precursor frequencies and phenotypes of myelin-specific CD8+T cells in the peripheral blood of untreated MS patients and HLA allele-matched healthy controls. In parallel, CD8+T cell responses against immunodominant influenza epitopes were also measured. There were no differences in ex vivo frequencies of tetramer-positive myelin-specific CD8+T cells between MS patients and control subjects. An increased proportion of myelin-specific CD8+T cells in MS patients exhibited a memory phenotype and expressed CD20 compared to control subjects, while there were no phenotypic differences observed among influenza-specific CD8+T cells. Longitudinal assessments were also measured in a subset of MS patients subsequently treated with anti-CD20 monoclonal antibody therapy. The proportion of memory and CD20+CD8+T cells specific for certain myelin but not influenza epitopes was significantly reduced following anti-CD20 treatment. This study, representing a characterization of unmanipulated myelin-reactive CD8+T cells in MS, indicates these cells may be attractive targets in MS therapy.

scholarly journals Identification of Rotavirus VP6-Specific CD4+ T Cell Epitopes in a G1P[8] Human Rotavirus-Infected Rhesus Macaque

2008 ◽  
Vol 1 ◽  
pp. VRT.S563 ◽  
Author(s):  
Wei Zhao ◽  
Bapi Pahar ◽  
Karol Sestak
Keyword(s):  
T Cell ◽  
Rhesus Macaques ◽  
Immunoglobulin A ◽  
Cd4 T Cell ◽  
T Cell Epitopes ◽  
Primate Model ◽  
Human Rotavirus ◽  
Ifn Γ ◽  
Rotavirus Vp6

A non-human primate model was used to evaluate its potential for identification of rotavirus viral protein 6 (VP6) CD4+ T cell epitopes. Four juvenile rhesus macaques were inoculated with a mixed inoculum (G1P[8] and G9P[8]) of human rotaviruses. Infection accompanied by G1P[8] shedding was achieved in the two macaques that had no rotavirus immunoglobulin A (IgA) in plasma. To measure the interferon gamma (IFN-γ) and tumor necrosis factor (TNF) anti-viral cytokines produced by peripheral CD4+ cells that recognize VP6 epitopes, whole blood cells from one infected macaque were stimulated in vitro with VP6 peptides. Stimulation with peptide pools derived from the simian rotavirus VP6161–395 region revealed reactivity of CD4+ T cells with the VP6281–331 domain. A VP6301–315 region was identified as the epitope responsible for IFN-γ production while a broader VP6293–327 domain was linked to TNF production. These results suggest that human rotavirus-infected macaques can be used for identification of additional epitopes and domains to address specific questions related to the development of pediatric vaccines.

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