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 ◽  
...  

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.

2021 ◽  
Vol 6 (57) ◽  
pp. eabg6461
Author(s):  
Benedikt Agerer ◽  
Maximilian Koblischke ◽  
Venugopal Gudipati ◽  
Luis Fernando Montaño-Gutierrez ◽  
Mark Smyth ◽  
...  

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.


2020 ◽  
Author(s):  
Carlos Wert-Carvajal ◽  
Rubén Sánchez-García ◽  
José R Macías ◽  
Rebeca Sanz-Pamplona ◽  
Almudena Méndez Pérez ◽  
...  

AbstractMotivationLack of a dedicated integrated pipeline for neoantigen discovery in mice hinders cancer immunotherapy research. Novel sequential approaches through recurrent neural networks can improve the accuracy of T-cell epitope immunogenicity predictions in mice and a simplified variant selection process can reduce operational requirements.ResultsWe have developed a web server tool (NAP-CNB) for a full and automatic pipeline, based on recurrent neural networks, able to predict putative neoantigens from tumoral RNA sequencing reads. The developed software is able to estimate H-2 peptide ligands, with an AUC of 0.95, directly from tumor samples. As a proof-of-concept, we used the B16 melanoma model to test the predictive capabilities of the system and we report its putative neoantigens.Availability and implementationNAP-CNB web server is freely available at http://biocomp.cnb.csic.es/NeoantigensApp/ with scripts and datasets accessible through the download section.


Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 130
Author(s):  
Eleonora Cimini ◽  
Germana Grassi ◽  
Alessia Beccacece ◽  
Rita Casetti ◽  
Concetta Castilletti ◽  
...  

γδ T cells are innate cells able to quickly eliminate pathogens or infected/tumoral cells by their antiviral and adjuvancy activities. The role of γδ T cells during Dengue Viral Infection (DENV) infection is not fully elucidated. Nevertheless, human primary γδ T cells have been shown to kill in vitro DENV-infected cells, thus highlighting their possible antiviral function. The aim of this work was to characterize the phenotype and function of Vδ2 T cells in DENV patients. Fifteen DENV patients were enrolled for this study and peripheral blood mononuclear cells (PBMC) were used to analyze Vδ2-T-cell frequency, differentiation profile, activation/exhaustion status, and functionality by multiparametric flow cytometry. Our data demonstrated that DENV infection was able to significantly reduce Vδ2-T-cell frequency and to increase their activation (CD38 and HLA-DR) and exhaustion markers (PD-1 and TIM-3). Furthermore, Vδ2 T cells showed a reduced capability to produce IFN-γ after phosphoantigenic stimulation that can be associated to TIM-3 expression. Several studies are needed to depict the possible clinical impact of γδ-T-cell impairment on disease severity and to define the antiviral and immunoregulatory activities of γδ T cells in the first phases of infection.


2021 ◽  
Author(s):  
Rubén Sánchez-García ◽  
José R Macías ◽  
Rebeca Sanz-Pamplona ◽  
Almudena Méndez-Pérez ◽  
Ramon Alemany ◽  
...  

Abstract Lack of a dedicated integrated pipeline for neoantigen discovery in mice hinders cancer immunotherapy research. Novel sequential approaches through recurrent neural networks can improve the accuracy of T-cell epitope immunogenicity predictions in mice, and a simplified variant selection process can reduce operational requirements. We have developed a web server tool (NAP-CNB) for a full and automatic pipeline based on recurrent neural networks, to predict putative neoantigens from tumoral RNA sequencing reads. The developed software can estimate H-2 peptide ligands, with an AUC of 0.95, directly from tumor samples. As a proof-of-concept, we used the B16 melanoma model to test the system’s predictive capabilities, and we report its putative neoantigens. NAP-CNB web server is freely available at http://biocomp.cnb.csic.es/NeoantigensApp/ with scripts and datasets accessible through the download section.


Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1173-1173
Author(s):  
Nora Mirza ◽  
Manfred Zierhut ◽  
Andreas Korn ◽  
Antje Bornemann ◽  
Christoph Simon ◽  
...  

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.


2017 ◽  
Author(s):  
Morten Nielsen ◽  
Tim Connelley ◽  
Nicola Ternette

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.


Author(s):  
Elahe Akbari ◽  
Kimia Kardani ◽  
Ali Namvar ◽  
Soheila Ajdary ◽  
Esmat Mirabzadeh Ardakani ◽  
...  

Vaccines ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 29
Author(s):  
Laia Bosch-Camós ◽  
Elisabet López ◽  
María Jesús Navas ◽  
Sonia Pina-Pedrero ◽  
Francesc Accensi ◽  
...  

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.


Blood ◽  
2012 ◽  
Vol 119 (11) ◽  
pp. 2443-2451 ◽  
Author(s):  
Tatiana Akimova ◽  
Ulf H. Beier ◽  
Yujie Liu ◽  
Liqing Wang ◽  
Wayne W. Hancock

Abstract Clinical and experimental studies show that inhibition of histone/protein deacetylases (HDAC) can have important anti-neoplastic effects through cytotoxic and proapoptotic mechanisms. There are also increasing data from nononcologic settings that HDAC inhibitors (HDACi) can exhibit useful anti-inflammatory effects in vitro and in vivo, unrelated to cytotoxicity or apoptosis. These effects can be cell-, tissue-, or context-dependent and can involve modulation of specific inflammatory signaling pathways as well as epigenetic mechanisms. We review recent advances in the understanding of how HDACi alter immune and inflammatory processes, with a particular focus on the effects of HDACi on T-cell biology, including the activation and functions of conventional T cells and the unique T-cell subset, composed of Foxp3+ T-regulatory cells. Although studies are still needed to tease out details of the various biologic roles of individual HDAC isoforms and their corresponding selective inhibitors, the anti-inflammatory effects of HDACi are already promising and may lead to new therapeutic avenues in transplantation and autoimmune diseases.


Author(s):  
Huw Davies ◽  
Ian Tarpey ◽  
Simon Stacey ◽  
Julian Hickling ◽  
Jennifer Bartholomew ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document