scholarly journals epitopepredict: A tool for integrated MHC binding prediction

2021 ◽  
Author(s):  
Damien Farrell

AbstractA key step in the cellular adaptive immune response is the presentation of antigen to T cells. During this process short peptides processed from self or foreign proteins may be presented on the surface bound to MHC molecules for binding to T cell receptors. Those that bind and activate an immune response are called epitopes. Computational prediction of T cell epitopes has many applications in vaccine design and immuno-diagnostics. This is the basis of immunoinformatics which allows in silico screening of peptides before experiments are performed. The most effective approach is to estimate the binding affinity of a given peptide fragment to MHC class I or II molecules. With the availability of whole genomes for many microbial species it is now feasible to computationally screen whole proteomes for candidate peptides. epitopepredict is a programmatic framework and command line tool designed to aid this process. It provides access to multiple binding prediction algorithms under a single interface and scales for whole genomes using multiple target MHC alleles. A web interface is provided to assist visualization and filtering of the results. The software is freely available under an open source license from https://github.com/dmnfarrell/epitopepredict

Gigabyte ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Damien Farrell

A key step in the cellular adaptive immune response is the presentation of antigens to T cells. Computational prediction of T cell epitopes has many applications in vaccine design and immuno-diagnostics. This is the basis of immunoinformatics, which allows in silico screening of peptides before experiments are performed. With the availability of whole genomes for many microbial species it is now feasible to computationally screen whole proteomes for candidate peptides. epitopepredict is a programmatic framework and command line tool designed to aid this process. It provides access to multiple binding prediction algorithms under a single interface and scales for whole genomes using multiple target MHC alleles. A web interface is provided to assist visualization and filtering of the results. The software is freely available under an open-source license from https://github.com/dmnfarrell/epitopepredict


Author(s):  
Alba Grifoni ◽  
John Sidney ◽  
Randi Vita ◽  
Bjoern Peters ◽  
Shane Crotty ◽  
...  

2021 ◽  
Vol 15 (8) ◽  
pp. 878-888
Author(s):  
Yang Liu ◽  
Xia-hui Ouyang ◽  
Zhi-Xiong Xiao ◽  
Le Zhang ◽  
Yang Cao

Background: T lymphocyte achieves an immune response by recognizing antigen peptides (also known as T cell epitopes) through major histocompatibility complex (MHC) molecules. The immunogenicity of T cell epitopes depends on their source and stability in combination with MHC molecules. The binding of the peptide to MHC is the most selective step, so predicting the binding affinity of the peptide to MHC is the principal step in predicting T cell epitopes. The identification of epitopes is of great significance in the research of vaccine design and T cell immune response. Objective: The traditional method for identifying epitopes is to synthesize and test the binding activity of peptide by experimental methods, which is not only time-consuming, but also expensive. In silico methods for predicting peptide-MHC binding emerge to pre-select candidate peptides for experimental testing, which greatly saves time and costs. By summarizing and analyzing these methods, we hope to have a better insight and provide guidance for future directions. Methods: Up to now, a number of methods have been developed to predict the binding ability of peptides to MHC based on various principles. Some of them employ matrix models or machine learning models based on the sequence characteristic embedded in peptides or MHC to predict the binding ability of peptides to MHC. Some others utilize the three-dimensional structural information of peptides or MHC, for example, by extracting three-dimensional structural information to construct a feature matrix or machine learning model, or directly using protein structure prediction, molecular docking to predict the binding mode of peptides and MHC. Results: Although the methods in predicting peptide-MHC binding based on the feature matrix or machine learning model can achieve high-throughput prediction, the accuracy of which depends heavily on the sequence characteristic of confirmed binding peptides. In addition, it cannot provide insights into the mechanism of antigen specificity. Therefore, such methods have certain limitations in practical applications. Methods in predicting peptide-MHC binding based on structural prediction or molecular docking are computationally intensive compared to the methods based on feature matrix or machine learning model and the challenge is how to predict a reliable structural model. Conclusion: This paper reviews the principles, advantages and disadvantages of the methods of peptide-MHC binding prediction and discussed the future directions to achieve more accurate predictions.


2003 ◽  
Vol 70 ◽  
pp. 31-38 ◽  
Author(s):  
Colin Watts ◽  
Daniela Mazzeo ◽  
Michelle A. West ◽  
Stephen P. Matthews ◽  
Doreen Keane ◽  
...  

The adaptive immune response depends on the creation of suitable peptides from foreign antigens for display on MHC molecules to T lymphocytes. Similarly, MHC-restricted display of peptides derived from self proteins results in the elimination of many potentially autoreactive T cells. Different proteolytic systems are used to generate the peptides that are displayed as T cell epitopes on class I compared with class II MHC molecules. In the case of class II MHC molecules, the proteases that reside within the endosome/lysosome system of antigen-presenting cells are responsible; surprisingly, however, there are relatively few data on which enzymes are involved. Recently we have asked whether proteolysis is required simply in a generic sense, or whether the action of particular enzymes is needed to generate specific class II MHC-associated T cell epitopes. Using the recently identified mammalian asparagine endopeptidase as an example, we review recent evidence that individual enzymes can make clear and non-redundant contributions to MHC-restricted peptide display.


Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 30
Author(s):  
Perrine Pégorier ◽  
Morgane Bertignac ◽  
Viviane Nguefack Ngoune ◽  
Géraldine Folch ◽  
Joumana Jabado-Michaloud ◽  
...  

The adaptive immune response provides the vertebrate immune system with the ability to recognize and remember specific pathogens to generate immunity, and mount stronger attacks each time the pathogen is encountered. T cell receptors are the antigen receptors of the adaptive immune response expressed by T cells, which specifically recognize processed antigens, presented as peptides by the highly polymorphic major histocompatibility (MH) proteins. T cell receptors (TR) are divided into two groups, αβ and γδ, which express distinct TR containing either α and β, or γ and δ chains, respectively. The TRα locus (TRA) and TRδ locus (TRD) of bovine (Bos taurus) and the sheep (Ovis aries) have recently been described and annotated by IMGT® biocurators. The aim of the present study is to present the results of the biocuration and to compare the genes of the TRA/TRD loci among these ruminant species based on the Homo sapiens repertoire. The comparative analysis shows similarities but also differences, including the fact that these two species have a TRA/TRD locus about three times larger than that of humans and therefore have many more genes which may demonstrate duplications and/or deletions during evolution.


2019 ◽  
Vol 92 ◽  
pp. 322-330 ◽  
Author(s):  
Yeny Leal ◽  
Janet Velazquez ◽  
Liz Hernandez ◽  
Jaya Kumari Swain ◽  
Alianet Rodríguez Rodríguez ◽  
...  

2019 ◽  
Vol 116 (6) ◽  
pp. 2312-2317 ◽  
Author(s):  
Emmanuelle Coque ◽  
Céline Salsac ◽  
Gabriel Espinosa-Carrasco ◽  
Béla Varga ◽  
Nicolas Degauque ◽  
...  

Adaptive immune response is part of the dynamic changes that accompany motoneuron loss in amyotrophic lateral sclerosis (ALS). CD4+T cells that regulate a protective immunity during the neurodegenerative process have received the most attention. CD8+T cells are also observed in the spinal cord of patients and ALS mice although their contribution to the disease still remains elusive. Here, we found that activated CD8+T lymphocytes infiltrate the central nervous system (CNS) of a mouse model of ALS at the symptomatic stage. Selective ablation of CD8+T cells in mice expressing the ALS-associated superoxide dismutase-1 (SOD1)G93Amutant decreased spinal motoneuron loss. Using motoneuron-CD8+T cell coculture systems, we found that mutant SOD1-expressing CD8+T lymphocytes selectively kill motoneurons. This cytotoxicity activity requires the recognition of the peptide-MHC-I complex (where MHC-I represents major histocompatibility complex class I). Measurement of interaction strength by atomic force microscopy-based single-cell force spectroscopy demonstrated a specific MHC-I-dependent interaction between motoneuron andSOD1G93ACD8+T cells. Activated mutant SOD1 CD8+T cells produce interferon-γ, which elicits the expression of the MHC-I complex in motoneurons and exerts their cytotoxic function through Fas and granzyme pathways. In addition, analysis of the clonal diversity of CD8+T cells in the periphery and CNS of ALS mice identified an antigen-restricted repertoire of their T cell receptor in the CNS. Our results suggest that self-directed immune response takes place during the course of the disease, contributing to the selective elimination of a subset of motoneurons in ALS.


Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1027
Author(s):  
Nima Taefehshokr ◽  
Sina Taefehshokr ◽  
Bryan Heit

The current coronavirus disease 2019 (COVID-19) pandemic, a disease caused by severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), was first identified in December 2019 in China, and has led to thousands of mortalities globally each day. While the innate immune response serves as the first line of defense, viral clearance requires activation of adaptive immunity, which employs B and T cells to provide sanitizing immunity. SARS-CoV-2 has a potent arsenal of mechanisms used to counter this adaptive immune response through processes, such as T cells depletion and T cell exhaustion. These phenomena are most often observed in severe SARS-CoV-2 patients, pointing towards a link between T cell function and disease severity. Moreover, neutralizing antibody titers and memory B cell responses may be short lived in many SARS-CoV-2 patients, potentially exposing these patients to re-infection. In this review, we discuss our current understanding of B and T cells immune responses and activity in SARS-CoV-2 pathogenesis.


2020 ◽  
Vol 4 (7) ◽  
pp. 1526-1537
Author(s):  
David R. Gruber ◽  
Amanda L. Richards ◽  
Heather L. Howie ◽  
Ariel M. Hay ◽  
Jenna N. Lebedev ◽  
...  

Abstract Antibodies are typically thought of as the endpoint of humoral immunity that occur as the result of an adaptive immune response. However, affinity-matured antibodies can be present at the initiation of a new immune response, most commonly because of passive administration as a medical therapy. The current paradigm is that immunoglobulin M (IgM), IgA, and IgE enhance subsequent humoral immunity. In contrast, IgG has a “dual effect” in which it enhances responses to soluble antigens but suppresses responses to antigens on red blood cells (RBCs) (eg, immunoprophylaxis with anti-RhD). Here, we report a system in which passive antibody to an RBC antigen promotes a robust cellular immune response leading to endogenous CD4+ T-cell activation, germinal center formation, antibody secretion, and immunological memory. The mechanism requires ligation of Fcγ receptors on a specific subset of dendritic cells that results in CD4+ T-cell activation and expansion. Moreover, antibodies cross-enhance responses to a third-party antigen, but only if it is expressed on the same RBC as the antigen recognized by the antibody. Importantly, these observations were IgG subtype specific. Thus, these findings demonstrate that antibodies to RBC alloantigens can enhance humoral immunity in an IgG subtype-specific fashion and provide mechanistic elucidation of the enhancing effects.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 363-363 ◽  
Author(s):  
Tae Hae Han ◽  
Yucheng Tang ◽  
Yeon Hee Park ◽  
Jonathan Maynard ◽  
Pingchuan Li ◽  
...  

Abstract Individuals of advanced chronological age exhibit an impaired immune response to vaccines. This may be due to a reduction in the ratio of antigen naïve/memory CD4 and CD8 T cells and acquisition of functional defects in activated “helper” CD4 T cells (eg diminished CD40 ligand (CD40L) expression) during the aging process. The absence of the CD40L on activated CD4 helper T cells reduces the magnitude of expansion of antigen specific T and B cells induced by vaccination. In order to circumvent this defective response to vaccines among individuals in the fifth and sixth decades of life, our laboratory has developed an adenoviral vector (Ad-sig-TAA/ecdCD40L) vaccine which is designed to overcome the absence of CD40L expression in activated CD4 helper T cells in older individuals. The subcutaneous (sc) injection of this vector leads to the release of a fusion protein composed of a TAA linked to the extracellular domain (ecd) of the CD40L, which binds to the CD40 receptor on DCs, activates the DCs, and leads to the presentation of TAA fragments on Class I MHC. Two sc injections of the TAA/ecdCD40L protein as a booster following the sc administration of the Ad-sig-TAA/ecdCD40L vector (we call this the TAA/ecdCD40L VPP vaccine) expands the magnitude of the cellular and humoral immune response induced by the vector in 18 month old aged mice as well as in younger mice. In order to explore ways of further amplifying the immune response induced by this vaccine, we decided to test the feasibility of using this vaccine following treatments which reduce the number of T cells in the body of the test subject. We hypothesized that during states of chemotherapy or radiation induced lymphopenia, the number of negative regulatory CD4CD25FoxP3 T cells would be reduced, and all of the regulatory signals in the T cell compartment would be promoting expansion of T cells, thus creating an ideal state for vaccination. To test this hypothesis, we injected 100,000 cells from an established neoplastic cell line sc. Three days later, we administered myeloablative doses of total body irradiation (TBI) followed by a T cell depleted syngeneic bone marrow transplant (TCDBMT) to reconstitute neutrophil and platelet production. Three days following the TBI and TCDBMT, we intravenously infused donor lymphocytes (DLI) from a TAA/ ecdCD40L VPP vaccinated syngeneic donor. Four weeks later, we vaccinated the recipient mouse further with TAA/ecdCD40L sc injections. We tested this for a TAA composed of a junctional peptide from the p210Bcr-Abl protein of chronic myelogenous leukemia (CML) and for the E7 protein of the human papilloma virus (HPV). We found that in the case of the BcrAbl/ecdCD40L VPP vaccine, 50% of the mice treated with TBI, TCDBMT, ten million lymphocytes (DLI) from BcrAbl/ecdCD40L VPP vaccinated syngeneic donors followed in 4 weeks by 3 BcrAbl/ecdCD40L protein sc injections of the recipient test mouse, developed a complete response with the vaccination and that these mice remained disease free beyond 250 days after injection of the P210Bcr-Abl positive 32D leukemia cells, whereas C56BL/6J test mice treated with TBI and TCDBMT without DLI from vaccinated donors nor sc BcrAbl/ecdCD40L sc booster vaccination following injection with the p210Bcr-Abl positive 32D myeloid leukemia cell line all died by day 32. Mice treated with TBI, TCDBMT, DLI from unvaccinated donors followed by vaccination of the recipient with 3 sc BcrAbl/ecdCD40L protein injections exhibited a degree of leukemia suppression that was equal to mice receiving TBI, TCDBMT, DLI from a BcrAbl/ecdCD40L VPP vaccinated donor and BcrAbl/ecdCD40L vaccination. To test the effect of the TAA/ecdCD40L VPP vaccine against an antigen associated with an epithelial neoplasm, we injected 100,000 E7 positive TC-1 mouse cancer cells into syngeneic C57BL6J mice followed in 3–5 days by myeloablative doses of TBI and engrafting doses of TCDBMT. Three days later, the mice received 10 million spleen cells from syngeneic donor mice previously vaccinated with the E7/ecdCD40L VPP vaccine. Finally, 4 weeks later, the test mice received sc E7/ecdCD40L protein booster injections. The vaccinated mice achieved much greater degrees of tumor suppression than was seen following TBI and TCDBMT without DLI from vaccinated donors. These studies show that it is possible to induce a robust adaptive immune response by vaccination with the TAA/ecdCD40L VPP vaccine even in severely lymphopenic individuals.


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