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Journal articles on the topic 'Epitope'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Mylin, Lawrence M. "Context-Dependent Immunogenicity of an S206G-Substituted H-2Db-Restricted Simian Virus 40 Large T Antigen Epitope I Variant." Journal of Immunology 162, no. 4 (1999): 2171–79. http://dx.doi.org/10.4049/jimmunol.162.4.2171.

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Abstract SV40 large tumor Ag (Tag) contains four H-2b-restricted (I, II/III, IV, and V) CTL epitopes. A hierarchy exists among these CTL epitopes. CTL directed against epitopes I, II/III, and IV are readily detected following immunization of H-2b mice with SV40, Tag-transformed syngeneic cells, or a vaccinia recombinant that expresses full-length Tag, while epitope V-specific CTL are not. The mechanisms that define this hierarchy remain unknown. Initial studies have shown that the locations of epitopes I and V within SV40 Tag do not determine the immunological potencies of these epitopes. Like

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2

Potocnakova, Lenka, Mangesh Bhide, and Lucia Borszekova Pulzova. "An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction." Journal of Immunology Research 2016 (2016): 1–11. http://dx.doi.org/10.1155/2016/6760830.

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Identification of B-cell epitopes is a fundamental step for development of epitope-based vaccines, therapeutic antibodies, and diagnostic tools. Epitope-based antibodies are currently the most promising class of biopharmaceuticals. In the last decade, in-depth in silico analysis and categorization of the experimentally identified epitopes stimulated development of algorithms for epitope prediction. Recently, various in silico tools are employed in attempts to predict B-cell epitopes based on sequence and/or structural data. The main objective of epitope identification is to replace an antigen

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3

Moriki, Takanori, Ichiro N. Maruyama, Yusuke Yamaguchi, Atsuko Igari, Yasuo Ikeda, and Mitsuru Murata. "Identification of ADAMTS13 Epitopes Required for Binding to von Willebrand Factor Using Lambda Phage Surface Display." Blood 110, no. 11 (2007): 2707. http://dx.doi.org/10.1182/blood.v110.11.2707.2707.

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Abstract The metalloprotease ADAMTS13 cleaves multimeric von Willebrand factor (VWF) to regulate VWF-mediated thrombus formation. We planned to search core epitopes of ADAMTS13 that is required for its binding to VWF. We constructed a random cDNA fragment library expressing various peptides of ADAMTS13 on the surface of lambda phage and screened the library using immobilized VWF as a probe. After the first screening, the C-terminus of the spacer domain from Arg670 to Glu684 (termed as epitope-1) and the middle of the cysteine-rich domain from Arg484 to Arg507 (epitope-2) were determined as epi

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Tornyi, Ilona, Jozsef Lazar, Aladar Pettko-Szandtner, Eva Hunyadi-Gulyas, and Laszlo Takacs. "Epitomics: Analysis of Plasma C9 Epitope Heterogeneity in the Plasma of Lung Cancer Patients and Control Subjects." International Journal of Molecular Sciences 24, no. 18 (2023): 14359. http://dx.doi.org/10.3390/ijms241814359.

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The human proteome is more complex than the genetic code predicts it to be. Epitomics, or protein epitome profiling, is a tool for understanding sub-protein level variation. With the ultimate goal to explore C9 proteoforms and their relevance to lung cancer, here we report plasma C9 epitope-associated molecular heterogeneity in plasma samples of lung cancer patients and control subjects. We show three C9 epitopes (BSI0449, BSI0581, BSI0639) with markedly different association with lung cancer (“unaltered”, “upregulated” and “downregulated”). In order to exclude confounding effects, we show fir

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5

De-Simone, Salvatore G., Paloma Napoleão-Pêgo, Guilherme C. Lechuga, et al. "Mapping IgA Epitope and Cross-Reactivity between Severe Acute Respiratory Syndrome-Associated Coronavirus 2 and DENV." Vaccines 11, no. 12 (2023): 1749. http://dx.doi.org/10.3390/vaccines11121749.

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Background: The newly introduced COVID-19 vaccines have reduced disease severity and hospitalizations. However, they do not significantly prevent infection or transmission. In the same context, measuring IgM and IgG antibody levels is important, but it does not provide information about the status of the mucosal immune response. This article describes a comprehensive mapping of IgA epitopes of the S protein, its cross-reactivity, and the development of an ELISA-peptide assay. Methods: IgA epitope mapping was conducted using SPOT synthesis and sera from RT-qPCR COVID-19-positive patients. Speci

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Soto, Luis Fernando, David Requena, and Juan Ignacio Fuxman Bass. "Epitope-Evaluator: An interactive web application to study predicted T-cell epitopes." PLOS ONE 17, no. 8 (2022): e0273577. http://dx.doi.org/10.1371/journal.pone.0273577.

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Multiple immunoinformatic tools have been developed to predict T-cell epitopes from protein amino acid sequences for different major histocompatibility complex (MHC) alleles. These prediction tools output hundreds of potential peptide candidates which require further processing; however, these tools are either not graphical or not friendly for non-programming users. We present Epitope-Evaluator, a web tool developed in the Shiny/R framework to interactively analyze predicted T-cell epitopes. Epitope-Evaluator contains six tools providing the distribution of epitopes across a selected set of MH

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7

Mylin, Lawrence M., Todd D. Schell, Debra Roberts, et al. "Quantitation of CD8+ T-Lymphocyte Responses to Multiple Epitopes from Simian Virus 40 (SV40) Large T Antigen in C57BL/6 Mice Immunized with SV40, SV40 T-Antigen-Transformed Cells, or Vaccinia Virus Recombinants Expressing Full-Length T Antigen or Epitope Minigenes." Journal of Virology 74, no. 15 (2000): 6922–34. http://dx.doi.org/10.1128/jvi.74.15.6922-6934.2000.

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ABSTRACT The cytotoxic T-lymphocyte response to wild-type simian virus 40 large tumor antigen (Tag) in C57BL/6 (H2b ) mice is directed against three H2-Db -restricted epitopes, I, II/III, and V, and oneH2-Kb -restricted epitope, IV. Epitopes I, II/III, and IV are immunodominant, while epitope V is immunorecessive. We investigated whether this hierarchical response was established in vivo or was due to differential expansion in vitro by using direct enumeration of CD8+ T lymphocytes with Tag epitope/major histocompatibility complex class I tetramers and intracellular gamma interferon staining.

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8

Ando, Takao, Rauf Latif, Samira Daniel, Katsumi Eguchi, and Terry F. Davies. "Dissecting Linear and Conformational Epitopes on the Native Thyrotropin Receptor." Endocrinology 145, no. 11 (2004): 5185–93. http://dx.doi.org/10.1210/en.2004-0789.

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Abstract The TSH receptor (TSHR) is the primary antigen in Graves’ disease. In this condition, autoantibodies to the TSHR that have intrinsic thyroid-stimulating activity develop. We studied the epitopes on the native TSHR using polyclonal antisera and monoclonal antibodies (mAbs) derived from an Armenian hamster model of Graves’ disease. Of 14 hamster mAbs analyzed, five were shown to bind to conformational epitopes including one mAb with potent thyroid-stimulating activity. Overlapping conformational epitopes were determined by cell-binding competition assays using fluorescently labeled mAbs

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Singh, Niraj K., Anuj Tyagi, Sumit Singhal, Anjay, Yogendra Singh Jadoun, and Anuradha Kumari. "Bio-Computational Prediction of Novel Epitopes on VP2 Protein of Infectious Bursal Disease Virus." Journal of Advances in Microbiology 24, no. 5 (2024): 26–39. http://dx.doi.org/10.9734/jamb/2024/v24i5824.

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Aim: Recently, many viral Immunogenic peptides or epitopes have been used as potential vaccine and also immuno-diagnostic candidates. In this study, we predicted different epitopic peptides on VP2 protein of infectious bursal disease virus (IBDV) using bioinformatics tools, which can be potential vaccine as well as diagnostic candidate for IBD, in future. Study Design: In the present study, B-cell epitopes (linear or continuous, and conformational) and T-cell epitopes were predicted on VP2 protein. Place and Duration of Study: Bihar Animal Sciences University, Patna, and Guru Angad Dev Veterin

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10

Lim, Li Cen, Yee Ying Lim, and Yee Siew Choong. "Data curation to improve the pattern recognition performance of B-cell epitope prediction by support vector machine." Pure and Applied Chemistry 93, no. 5 (2021): 571–77. http://dx.doi.org/10.1515/pac-2020-1107.

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Abstract B-cell epitope will be recognized and attached to the surface of receptors in B-lymphocytes to trigger immune response, thus are the vital elements in the field of epitope-based vaccine design, antibody production and therapeutic development. However, the experimental approaches in mapping epitopes are time consuming and costly. Computational prediction could offer an unbiased preliminary selection to reduce the number of epitopes for experimental validation. The deposited B-cell epitopes in the databases are those with experimentally determined positive/negative peptides and some are

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11

Liu, Jinyan, Bonnie A. Ewald, Diana M. Lynch, Anjali Nanda, Shawn M. Sumida, and Dan H. Barouch. "Modulation of DNA Vaccine-Elicited CD8+ T-Lymphocyte Epitope Immunodominance Hierarchies." Journal of Virology 80, no. 24 (2006): 11991–97. http://dx.doi.org/10.1128/jvi.01348-06.

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ABSTRACT Generating broad cellular immune responses against a diversity of viral epitopes is a major goal of current vaccine strategies for human immunodeficiency virus type 1 (HIV-1) and other pathogens. Virus-specific CD8+ T-lymphocyte responses, however, are often highly focused on a very limited number of immunodominant epitopes. For an HIV-1 vaccine, the breadth of CD8+ T-lymphocyte responses may prove to be critical as a result of the need to cover a wide diversity of viral isolates in the population and to limit viral escape from dominant epitope-specific T lymphocytes. Here we show tha

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12

Kahn, S. J., and M. Wleklinski. "The surface glycoproteins of Trypanosoma cruzi encode a superfamily of variant T cell epitopes." Journal of Immunology 159, no. 9 (1997): 4444–51. http://dx.doi.org/10.4049/jimmunol.159.9.4444.

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Abstract Trypanosoma cruzi is an obligate intracellular protozoan parasite. During mammalian infection, extracellular and intracellular parasites simultaneously express multiple members of a polymorphic surface protein superfamily. The effect of this extensive surface protein polymorphism on the mammalian host T cell response is not known. In this report, we identified a surface protein MHC class II-restricted T cell epitope (epitope 1), and cloned 10 surface protein cDNAs that encode epitope 1 variants. All these cDNA variant epitopes were processed and presented to T cells, and some function

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13

Hayashi, Hiroki, and Tsutomu Kishi. "A Set of Plasmid-Based Modules for Easy Switching of C-Terminal Epitope Tags in Saccharomyces cerevisiae." Microorganisms 9, no. 12 (2021): 2505. http://dx.doi.org/10.3390/microorganisms9122505.

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Epitope tagging is a powerful strategy for analyzing the functions of targeted proteins. The use of this strategy has become more convenient with the development of the epitope switch, which is another type of epitope tagging designed to convert the previously tagged epitopes on the chromosome to other epitopes of interest. Various modules for C-terminal epitope switching have been developed and amplified using the one-step polymerase chain reaction (PCR) method before transformation. However, PCR amplification occasionally generates mutations that affect the fidelity of epitope switching. Her

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14

Kwon, Hyeji, Soobon Ko, Kyungsoo Ha, Jungjoon K. Lee, and Yoonjoo Choi. "Assessing the predictive ability of computational epitope prediction methods on Fel d 1 and other allergens." PLOS ONE 19, no. 8 (2024): e0306254. http://dx.doi.org/10.1371/journal.pone.0306254.

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While computational epitope prediction methods have found broad application, their use, specifically in allergy-related contexts, remains relatively less explored. This study benchmarks several publicly available epitope prediction tools, focusing on the allergenic IgE and T-cell epitopes of Fel d 1, an extensively studied allergen. Using a variety of tools accessible via the Immune Epitope Database (IEDB) and other resources, we evaluate their ability to identify the known linear IgE and T-cell epitopes of Fel d 1. Our results show a limited effectiveness for B-cell epitope prediction methods

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15

Molero-Abraham, Magdalena, John-Paul Glutting, Darren R. Flower, Esther M. Lafuente, and Pedro A. Reche. "EPIPOX: Immunoinformatic Characterization of the Shared T-Cell Epitome between Variola Virus and Related Pathogenic Orthopoxviruses." Journal of Immunology Research 2015 (2015): 1–11. http://dx.doi.org/10.1155/2015/738020.

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Concerns that variola viruses might be used as bioweapons have renewed the interest in developing new and safer smallpox vaccines. Variola virus genomes are now widely available, allowing computational characterization of the entire T-cell epitome and the use of such information to develop safe and yet effective vaccines. To this end, we identified 124 proteins shared between various species of pathogenic orthopoxviruses including variola minor and major, monkeypox, cowpox, and vaccinia viruses, and we targeted them for T-cell epitope prediction. We recognized 8,106, and 8,483 unique class I a

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16

Bautista, Enrico, Young Hyun Jung, Manuela Jaramillo, et al. "AutoPepVax, a Novel Machine-Learning-Based Program for Vaccine Design: Application to a Pan-Cancer Vaccine Targeting EGFR Missense Mutations." Pharmaceuticals 17, no. 4 (2024): 419. http://dx.doi.org/10.3390/ph17040419.

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The current epitope selection methods for peptide vaccines often rely on epitope binding affinity predictions, prompting the need for the development of more sophisticated in silico methods to determine immunologically relevant epitopes. Here, we developed AutoPepVax to expedite and improve the in silico epitope selection for peptide vaccine design. AutoPepVax is a novel program that automatically identifies non-toxic and non-allergenic epitopes capable of inducing tumor-infiltrating lymphocytes by considering various epitope characteristics. AutoPepVax employs random forest classification and

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17

Caoili, Salvador Eugenio C. "Expressing Redundancy among Linear-Epitope Sequence Data Based on Residue-Level Physicochemical Similarity in the Context of Antigenic Cross-Reaction." Advances in Bioinformatics 2016 (May 4, 2016): 1–13. http://dx.doi.org/10.1155/2016/1276594.

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Epitope-based design of vaccines, immunotherapeutics, and immunodiagnostics is complicated by structural changes that radically alter immunological outcomes. This is obscured by expressing redundancy among linear-epitope data as fractional sequence-alignment identity, which fails to account for potentially drastic loss of binding affinity due to single-residue substitutions even where these might be considered conservative in the context of classical sequence analysis. From the perspective of immune function based on molecular recognition of epitopes, functional redundancy of epitope data (FRE

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18

Lohnas, Gerald L., Steven F. Roberts, Aprile Pilon, and Alfonso Tramontano. "Epitope-Specific Antibody and Suppression of Autoantibody Responses Against a Hybrid Self Protein." Journal of Immunology 161, no. 12 (1998): 6518–25. http://dx.doi.org/10.4049/jimmunol.161.12.6518.

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Abstract This study addresses the relationship of epitope-specific Ab responses and alternative autoantibody responses in a model system in which an antigenized self protein serves as the carrier for a defined heterologous B cell epitope. Ubiquitin, a nonimmunogenic self protein, was engineered to present heterologous B and T cell epitopes in the recombinant molecule. Fusion to the C terminus introduced a universal T cell epitope from a Mycobacterium tuberculosis Ag. The B cell epitope was created by inserting a 12-residue loop sequence of HIV-1 gp120 at a surface-exposed position of ubiquitin

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Friedrich, Thomas C., Adrian B. McDermott, Matthew R. Reynolds, et al. "Consequences of Cytotoxic T-Lymphocyte Escape: Common Escape Mutations in Simian Immunodeficiency Virus Are Poorly Recognized in Naïve Hosts." Journal of Virology 78, no. 18 (2004): 10064–73. http://dx.doi.org/10.1128/jvi.78.18.10064-10073.2004.

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ABSTRACT Cytotoxic T lymphocytes (CTL) are associated with control of immunodeficiency virus infection but also select for variants that escape immune recognition. Declining frequencies of epitope-specific CTL frequencies have been correlated with viral escape in individual hosts. However, escape mutations may give rise to new epitopes that could be recognized by CTL expressing appropriate T-cell receptors and thus still be immunogenic when escape variants are passed to individuals expressing the appropriate major histocompatibility complex class I molecules. To determine whether peptide ligan

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Yu, Simiao, Xinhui Yu, Yantong Zhou, Nan Chen, Peng Wang, and Shaojie Bi. "Application of Immunoinformatics for Efficient Epitope-Based Peptide Vaccine Development." Scholars Journal of Engineering and Technology 12, no. 10 (2024): 298–306. http://dx.doi.org/10.36347/sjet.2024.v12i10.001.

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As global public health continues to face evolving challenges, developing effective and safe vaccines has become increasingly crucial, with the design of epitope-based vaccines representing a significant breakthrough in the field. The design of epitope vaccines generally involves utilizing immunoinformatics tools and techniques to analyze known or newly identified amino acid sequences, allowing for pre-selecting and identifying potential dominant epitopes. Subsequently, peptide vaccines containing these epitopes are synthesized through chemical or genetic engineering. The rapid progress in Imm

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Thorle, Shruti Sanjay, Mahadev Asaram Jadhav, Dipak Pandit Chavan, and Shivani Sunil Dhadge. "Development of epitope-based vaccine to prevent Marburg virus infection: an in silico approach." EUREKA: Life Sciences, no. 2 (June 28, 2024): 3–10. http://dx.doi.org/10.21303/2504-5695.2024.003411.

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Marburg virus (MARV) is one of the deadliest zoonotic viruses, causing severe hemorrhagic fever in humans with high mortality rates. The development of an effective vaccine is crucial to prevent potential Marburg virus outbreaks. In this study, an in silico approach was employed to design an epitope-based vaccine to prevent MARV infections. The MARV proteins nominating NP, VP24, VP35, VP30, VP40, GP & Polymerase L was analyzed for antigenicity and non-allergenicity prediction, among these proteins VP30 protein has a 0.5636 (Probable Antigen) score and it was non-allergen. For that reason,

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Savsani, Kush, Gabriel Jabbour, and Sivanesan Dakshanamurthy. "A New Epitope Selection Method: Application to Design a Multi-Valent Epitope Vaccine Targeting HRAS Oncogene in Squamous Cell Carcinoma." Vaccines 10, no. 1 (2021): 63. http://dx.doi.org/10.3390/vaccines10010063.

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We developed an epitope selection method for the design of MHC targeting peptide vaccines. The method utilizes predictions for several clinical checkpoint filters, including binding affinity, immunogenicity, antigenicity, half-life, toxicity, IFNγ release, and instability. The accuracy of the prediction tools for these filter variables was confirmed using experimental data obtained from the Immune Epitope Database (IEDB). We also developed a graphical user interface computational tool called ‘PCOptim’ to assess the success of an epitope filtration method. To validate the filtration methods, we

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Mazumder, Lincon, Md Rakibul Hasan, Kanij Fatema, Shamima Begum, Abul Kalam Azad, and Mohammad Ariful Islam. "Identification of B and T Cell Epitopes to Design an Epitope-Based Peptide Vaccine against the Cell Surface Binding Protein of Monkeypox Virus: An Immunoinformatics Study." Journal of Immunology Research 2023 (February 22, 2023): 1–14. http://dx.doi.org/10.1155/2023/2274415.

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Background. Although the monkeypox virus-associated illness was previously confined to Africa, recently, it has started to spread across the globe and become a significant threat to human lives. Hence, this study was designed to identify the B and T cell epitopes and develop an epitope-based peptide vaccine against this virus’s cell surface binding protein through an in silico approach to combat monkeypox-associated diseases. Results. The analysis revealed that the cell surface binding protein of the monkeypox virus contains 30 B cell and 19 T cell epitopes within the given parameter. Among th

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Abesamis, Lyn Marielle I., Evan Gilles A. Aliping, Fritz Khrystian Gabriel H. Armada, et al. "In Silico Comparative Analysis of Predicted B Cell Epitopes against Dengue Virus (Serotypes 1–4) Isolated from the Philippines." Vaccines 10, no. 8 (2022): 1259. http://dx.doi.org/10.3390/vaccines10081259.

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Dengue is a viral mosquito-borne disease that rapidly spreads in tropical and subtropical countries, including the Philippines. One of its most distinguishing characteristics is the ability of the Dengue Virus (DENV) to easily surpass the innate responses of the body, thus activating B cells of the adaptive immunity to produce virus-specific antibodies. Moreover, Dengvaxia® is the only licensed vaccine for DENV, but recent studies showed that seronegative individuals become prone to increased disease severity and hospitalization. Owing to this limitation of the dengue vaccine, this study deter

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Manuel, Edwin R., William A. Charini, Pritha Sen, et al. "Contribution of T-Cell Receptor Repertoire Breadth to the Dominance of Epitope-Specific CD8+ T-Lymphocyte Responses." Journal of Virology 80, no. 24 (2006): 12032–40. http://dx.doi.org/10.1128/jvi.01479-06.

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ABSTRACT Dominant epitope-specific CD8+ T-lymphocyte responses play a central role in controlling viral spread. We explored the basis for the development of this focused immune response in simian immunodeficiency virus (SIV)- and simian-human immunodeficiency virus (SHIV)-infected rhesus monkeys through the use of two dominant (p11C and p199RY) and two subdominant (p68A and p56A) epitopes. Using real-time PCR to quantitate T-cell receptor (TCR) variable region beta (Vβ) family usage, we show that CD8+ T-lymphocyte populations specific for dominant epitopes are characterized by a diverse Vβ rep

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Chow, SN, KW Chen, SL Su, J. Tung, and CY Lee. "Generation and epitope analysis of thyroid stimulating hormone‐specific monoclonal antibodies for enzyme immunoassays." Biotechnology and Applied Biochemistry 10, no. 2 (1988): 137–42. http://dx.doi.org/10.1111/j.1470-8744.1988.tb00009.x.

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By using an improved hybridoma technique with a semisolid medium of methylcellulose for initial cloning, numerous high affinity monoclonal antibodies against human thyroid stimulating hormone (TSH) were generated. These antibodies were characterized with respect to their subunit and epitope specificity. Epitope analysis of antibodies specific to the beta‐subunit of TSH was performed by a sandwich pairing procedure. Based on the results of this analysis, it was concluded that there are four distinct TSH‐specific epitopes on the beta‐subunit of TSH; these are designated a, b, c, and ab. The five

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Lautscham, Georg, Sabine Mayrhofer, Graham Taylor, et al. "Processing of a Multiple Membrane Spanning Epstein-Barr Virus Protein for Cd8+T Cell Recognition Reveals a Proteasome-Dependent, Transporter Associated with Antigen Processing–Independent Pathway." Journal of Experimental Medicine 194, no. 8 (2001): 1053–68. http://dx.doi.org/10.1084/jem.194.8.1053.

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Epstein-Barr virus (EBV) latent membrane protein (LMP)2 is a multiple membrane spanning molecule which lacks ectodomains projecting into the lumen of the endoplasmic reticulum (ER). Human CD8+ cytotoxic T lymphocytes (CTL)s recognize a number of epitopes within LMP2. Assays with epitope-specific CTLs in two different cell backgrounds lacking the transporter associated with antigen processing (TAP) consistently show that some, but not all, LMP2 epitopes are presented in a TAP-independent manner. However, unlike published examples of TAP-independent processing from endogenously expressed antigen

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Mufida, Diana Chusna, Ayu Munawaroh Aziz, and Nurrul Izza Misturiansyah. "Potential of B-Cell Epitopes Protein Ag85 Complex Mycobacterium Tuberculosis as Serodiagnostic Antigen of Tuberculosis by in Silico Study." Journal of Biomedicine and Translational Research 9, no. 1 (2023): 7–13. http://dx.doi.org/10.14710/jbtr.v9i1.16379.

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Background: The high case of tuberculosis which isn't followed by good detection becomes an urgency for the diagnostic developments. One of them with immunodiagnostic principle uses B-cell Ag85 complex epitope. The design of the diagnostic epitope was performed by mapping the B cell epitope used in silico studies.Objective: The purpose of this research is to analyze antigenicity, physicochemical which affect immunogenicity, and homology of B-cell Ag85 complex epitope with the strain which circulates in Indonesia. Methods: The samples used were taken from the NCBI protein bank with access numbe

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Kim, Ae, Isamu Hartman, David Lanar, Tatiana Boronina, Robert Cole, and Scheherazade Sadegh-Nasseri. "The hierarchy of two different immunodominant epitopes influences CD4+ T cell responses (APP5P.112)." Journal of Immunology 194, no. 1_Supplement (2015): 183.14. http://dx.doi.org/10.4049/jimmunol.194.supp.183.14.

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Abstract A cell-free antigen processing system for MHC class II was recently reported that has proved to be effective in identifying physiologically relevant CD4+ T cell epitopes from proteins (Hartman/Kim, et al. Nat Med. 16, pp1333-40 (2010)). This system has also provided insights into the mechanism of epitope selection (Kim, et al. Nat Commun. 5:5369 (2014)). We applied this system to a mixture of two different antigens, H5N1-HA1 and LSA-NRC of malaria to examine if there would be a competition for epitope capture. While each dominant epitope from either protein was identified in the syste

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Lee, Sujin, Hoyin Mok, Daivd Wright, and James E. Crowe. "Modulation of the CD8+ T cell response to subdominant epitopes of respiratory syncytial virus by deletion of an immunodominant epitope (43.9)." Journal of Immunology 178, no. 1_Supplement (2007): S37—S38. http://dx.doi.org/10.4049/jimmunol.178.supp.43.9.

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Abstract Cytotoxic T lymphocytes (CTLs) are critical for control of respiratory syncytial virus (RSV) infection in humans and mice. Recently, we identified a new H-2Kd- restricted subdominant epitope in the RSV M2 protein. This finding allowed us to study the frequency of T lymphocytes responding two H-2Kd-restricted epitopes, M282–90 and M2127–135, following RSV infection in both lymphoid and non-lymphoid tissues. The ratio of T lymphocytes during the peak CTL response to RSV infection that were specific for immunodominant or subdominant was approximately 3:1 in the spleen and 10:1 in the lun

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Yamada, Takashi, Hiroshi Uchiyama, Toshi Nagata, et al. "Protective Cytotoxic T Lymphocyte Responses Induced by DNA Immunization against Immunodominant and Subdominant Epitopes ofListeria monocytogenes Are Noncompetitive." Infection and Immunity 69, no. 5 (2001): 3427–30. http://dx.doi.org/10.1128/iai.69.5.3427-3430.2001.

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ABSTRACT Taking advantage of the fact that plasmid DNA encoding a single cytotoxic T lymphocyte (CTL) epitope can induce CTLs, we examined the influence of T-cell responses to dominant epitopes on those to a subdominant epitope derived from Listeria monocytogenes. Our data suggest that interaction between T cells against dominant and subdominant epitopes does not operate in the generation of the hierarchy. Furthermore, we found that a single dominant epitope is sufficient for the induction of protective immunity.

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Sanchez-Trincado, Jose L., Marta Gomez-Perosanz, and Pedro A. Reche. "Fundamentals and Methods for T- and B-Cell Epitope Prediction." Journal of Immunology Research 2017 (2017): 1–14. http://dx.doi.org/10.1155/2017/2680160.

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Adaptive immunity is mediated by T- and B-cells, which are immune cells capable of developing pathogen-specific memory that confers immunological protection. Memory and effector functions of B- and T-cells are predicated on the recognition through specialized receptors of specific targets (antigens) in pathogens. More specifically, B- and T-cells recognize portions within their cognate antigens known as epitopes. There is great interest in identifying epitopes in antigens for a number of practical reasons, including understanding disease etiology, immune monitoring, developing diagnosis assays

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Lin, Lin, Beverlie Baquir, Brandon Tan, et al. "Vaccine Dose Alters Immunodominant Epitopes and Cytokine Profile in Response to the Acinetobacter baumannii rOmpA Vaccine (52.12)." Journal of Immunology 188, no. 1_Supplement (2012): 52.12. http://dx.doi.org/10.4049/jimmunol.188.supp.52.12.

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Abstract Background: The rOmpA vaccine protects mice from lethal infection caused by extreme-drug-resistant (XDR) Acinetobacter baumannii. The role of dose and epitope in immunology of the rOmpA vaccine was explored. Methods: The rOmpA vaccine was epitope-mapped using overlapping peptides to stimulate splenocytes from mice administered varying vaccine doses. B cell epitopes were mapped by peptide immunoblotting. Results: Vaccination with rOmpA plus Al(OH)3 adjuvant induced IFN-γ, IL-4, and IL-17+ splenocytes. Epitope mapping revealed distinct T cell epitopes that induced IFNγ+, IL-4+, and IL-1

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Long, H. M., T. A. Haigh, N. H. Gudgeon, et al. "CD4+ T-Cell Responses to Epstein-Barr Virus (EBV) Latent-Cycle Antigens and the Recognition of EBV-Transformed Lymphoblastoid Cell Lines." Journal of Virology 79, no. 8 (2005): 4896–907. http://dx.doi.org/10.1128/jvi.79.8.4896-4907.2005.

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ABSTRACT There is considerable interest in the potential of Epstein-Barr virus (EBV) latent antigen-specific CD4+ T cells to act as direct effectors controlling EBV-induced B lymphoproliferations. Such activity would require direct CD4+ T-cell recognition of latently infected cells through epitopes derived from endogenously expressed viral proteins and presented on the target cell surface in association with HLA class II molecules. It is therefore important to know how often these conditions are met. Here we provide CD4+ epitope maps for four EBV nuclear antigens, EBNA1, -2, -3A, and -3C, and

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Tang, Xian, Wei Zhang, and Zheng Zhang. "Developing T Cell Epitope-Based Vaccines Against Infection: Challenging but Worthwhile." Vaccines 13, no. 2 (2025): 135. https://doi.org/10.3390/vaccines13020135.

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T cell epitope-based vaccines are designed to elicit long-lived pathogen-specific memory T cells that can quickly activate protective effector functions in response to subsequent infections. These vaccines have the potential to provide sustained protection against mutated variants, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which are increasingly capable of evading neutralizing antibodies. Recent advancements in epitope discovery, T cell receptor analysis, and bioinformatics have enabled the precise selection of epitopes and the sophisticated design of epitope-based

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He, Shudong, Jinlong Zhao, Walid Elfalleh, et al. "In Silico Identification and in Vitro Analysis of B and T-Cell Epitopes of the Black Turtle Bean (Phaseolus Vulgaris L.) Lectin." Cellular Physiology and Biochemistry 49, no. 4 (2018): 1600–1614. http://dx.doi.org/10.1159/000493496.

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Background/Aims: The incidence of lectin allergic disease is increasing in recent decades, and definitive treatment is still lacking. Identification of B and T-cell epitopes of allergen will be useful in understanding the allergen antibody responses as well as aiding in the development of new diagnostics and therapy regimens for lectin poisoning. In the current study, we mainly addressed these questions. Methods: Three-dimensional structure of the lectin from black turtle bean (Phaseolus vulgaris L.) was modeled using the structural template of Phytohemagglutinin from P. vulgaris (PHA-E, PDB I

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Goulder, P. J. R., A. K. Sewell, D. G. Lalloo, et al. "Patterns of Immunodominance in HIV-1–specific Cytotoxic T Lymphocyte Responses in Two Human Histocompatibility Leukocyte Antigens (HLA)-identical Siblings with HLA-A*0201 Are Influenced by Epitope Mutation." Journal of Experimental Medicine 185, no. 8 (1997): 1423–33. http://dx.doi.org/10.1084/jem.185.8.1423.

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Primary human immunodeficiency virus (HIV) infection is controlled principally by HIV-specific cytotoxic T lymphocytes (CTL) to a steady-state level of virus load, which strongly influences the ultimate rate of progression to disease. Epitope selection by CTL may be an important determinant of the degree of immune control over the virus. This report describes the CTL responses of two HLA-identical hemophiliac brothers who were exposed to identical batches of Factor VIII and became seropositive within 10 wk of one another. Both have HLA-A*0201. The CTL responses of the two siblings were very di

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Fischer, Marion F. S., James E. Crowe, and Jens Meiler. "Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods." PLOS Computational Biology 18, no. 12 (2022): e1010230. http://dx.doi.org/10.1371/journal.pcbi.1010230.

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Antibody epitope mapping of viral proteins plays a vital role in understanding immune system mechanisms of protection. In the case of class I viral fusion proteins, recent advances in cryo-electron microscopy and protein stabilization techniques have highlighted the importance of cryptic or ‘alternative’ conformations that expose epitopes targeted by potent neutralizing antibodies. Thorough epitope mapping of such metastable conformations is difficult but is critical for understanding sites of vulnerability in class I fusion proteins that occur as transient conformational states during viral a

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Biner, Daniel W., Jason S. Grosch, and Peter J. Ortoleva. "B-cell epitope discovery: The first protein flexibility-based algorithm–Zika virus conserved epitope demonstration." PLOS ONE 18, no. 3 (2023): e0262321. http://dx.doi.org/10.1371/journal.pone.0262321.

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Antibody-antigen interaction–at antigenic local environments called B-cell epitopes–is a prominent mechanism for neutralization of infection. Effective mimicry, and display, of B-cell epitopes is key to vaccine design. Here, a physical approach is evaluated for the discovery of epitopes which evolve slowly over closely related pathogens (conserved epitopes). The approach is 1) protein flexibility-based and 2) demonstrated with clinically relevant enveloped viruses, simulated via molecular dynamics. The approach is validated against 1) seven structurally characterized enveloped virus epitopes w

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Yuan, Tom Z., Ana G. Lujan Hernandez, Erica Keane, et al. "Rapid exploration of the epitope coverage produced by an Ebola survivor to guide the discovery of therapeutic antibody cocktails." Antibody Therapeutics 3, no. 3 (2020): 167–78. http://dx.doi.org/10.1093/abt/tbaa016.

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ABSTRACT Background Development of successful neutralizing antibodies is dependent upon broad epitope coverage to increase the likelihood of achieving therapeutic function. Recent advances in synthetic biology have allowed us to conduct an epitope binning study on a large panel of antibodies identified to bind to Ebola virus glycoprotein with only published sequences. Methods and Results A rapid, first-pass epitope binning experiment revealed seven distinct epitope families that overlapped with known structural epitopes from the literature. A focused set of antibodies was selected from represe

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Ostrowski, M., J. A. Galeota, A. M. Jar, K. B. Platt, F. A. Osorio, and O. J. Lopez. "Identification of Neutralizing and Nonneutralizing Epitopes in the Porcine Reproductive and Respiratory Syndrome Virus GP5 Ectodomain." Journal of Virology 76, no. 9 (2002): 4241–50. http://dx.doi.org/10.1128/jvi.76.9.4241-4250.2002.

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ABSTRACT After infection of swine with porcine reproductive and respiratory syndrome virus (PRRSV), there is a rapid rise of PRRSV-specific nonneutralizing antibodies (NNA), while neutralizing antibodies (NA) are detectable not sooner than 3 weeks later. To characterize neutralizing epitopes, we selected phages from a 12-mer phage display library using anti-PRRSV neutralizing monoclonal antibody (MAb) ISU25-C1. In addition, phages carrying peptides recognized by swine antibodies with high seroneutralizing titer were isolated after subtracting from the library those clones binding to swine anti

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Zhai, Yougang, Zhenyu Zhong, Mohammadreza Zariffard, Gregory Spear, and Liang Qiao. "BPV VLPs presenting HIV-1 epitopes from membrane-proximal external region of gp41 induced HIV-specific mucosal and systemic cross-clade neutralizing antibodies (P4507)." Journal of Immunology 190, no. 1_Supplement (2013): 179.16. http://dx.doi.org/10.4049/jimmunol.190.supp.179.16.

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Abstract Two conserved epitopes, located in the membrane-proximal external region (MPER) of gp41 of the human immunodeficiency virus type 1 (HIV-1) envelope spike, are promising targets for vaccine design in efforts to elicit 2F5 and 4E10-like anti-HIV-1 broadly neutralizing antibodies. Since most HIV-1 infections initiate at mucosal surfaces, the induction of mucosal neutralizing antibodies is necessary and of utmost importance to counteract HIV-1 infection. Here, we utilized a mucosal vaccine vector, bovine papillomavirus (BPV) virus-like particles (VLPs), as a platform to present HIV-1 neut

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Weidt, Gunnar, Olaf Utermöhlen, Jochen Heukeshoven, Fritz Lehmann-Grube, and Wolfgang Deppert. "Relationship Among Immunodominance of Single CD8+ T Cell Epitopes, Virus Load, and Kinetics of Primary Antiviral CTL Response." Journal of Immunology 160, no. 6 (1998): 2923–31. http://dx.doi.org/10.4049/jimmunol.160.6.2923.

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Abstract The primary CTL response of BALB/c mice infected with the lymphocytic choriomeningitis (LCM) virus strain WE is directed exclusively against one major epitope, n118, whereas a viral variant, ESC, that does not express n118 induces CTL against minor epitopes. We identified one minor epitope, g283, that induces primary lytic activity in ESC-infected mice. Infections of mice with WE and ESC were used to study the hierarchical control of a T cell response. Presentation of minor epitopes is not reduced in WE-infected cells. Generation of CTL against n118 does not suppress the generation of

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Tan, Swan, Andres Hazaet Gutiérrez, Phillip Charles Gauger, et al. "Quantifying the Persistence of Vaccine-Related T Cell Epitopes in Circulating Swine Influenza A Strains from 2013–2017." Vaccines 9, no. 5 (2021): 468. http://dx.doi.org/10.3390/vaccines9050468.

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When swine flu vaccines and circulating influenza A virus (IAV) strains are poorly matched, vaccine-induced antibodies may not protect from infection. Highly conserved T cell epitopes may, however, have a disease-mitigating effect. The degree of T cell epitope conservation among circulating strains and vaccine strains can vary, which may also explain differences in vaccine efficacy. Here, we evaluate a previously developed conserved T cell epitope-based vaccine and determine the persistence of T cell epitope conservation over time. We used a pair-wise homology score to define the conservation

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ELKHOLY, SHEREEN F. "Using Immunoinformatics to Design a mRNA Vaccine against the Spike Glycoprotein of SARS-CoV-2." Romanian Biotechnological Letters 26, no. 5 (2021): 2901–15. http://dx.doi.org/10.25083/rbl/26.5/2901.2915.

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The rapid outbreak of the new coronavirus SARS-COV-2 has created a major public health challenge. Immunoinformatics tools had a clear effect in tracking the genetic sequence of the virus and monitoring mutations and design vaccines that are effective enough to produce antibodies. In our study, we resorted to the emerging discipline of immunoinformatics in order to design a multi-epitope mRNA vaccine against the spike glycoprotein of SARS-CoV-2. We screened the B cell and T cell epitopes of the Spike glycoprotein. we used ABC pred server to predict B cell epitope in the spike glycoprotein seque

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Ma, Chenglie, Phyllis E. Whiteley, Patricia M. Cameron, et al. "Role of APC in the Selection of Immunodominant T Cell Epitopes." Journal of Immunology 163, no. 12 (1999): 6413–23. http://dx.doi.org/10.4049/jimmunol.163.12.6413.

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Abstract Following antigenic challenge, MHC-restricted T cell responses are directed against a few dominant antigenic epitopes. Here, evidence is provided demonstrating the importance of APC in modulating the hierarchy of MHC class II-restricted T cell responses. Biochemical analysis of class II:peptide complexes in B cells revealed the presentation of a hierarchy of peptides derived from the Ig self Ag. Functional studies of κ peptide:class II complexes from these cells indicated that nearly 20-fold more of an immunodominant epitope derived from κ L chains was bound to class II DR4 compared w

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Kaikkonen, Leena, Hilkka Lankinen, Irene Harjunpää, et al. "Acute-Phase-Specific Heptapeptide Epitope for Diagnosis of Parvovirus B19 Infection." Journal of Clinical Microbiology 37, no. 12 (1999): 3952–56. http://dx.doi.org/10.1128/jcm.37.12.3952-3956.1999.

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The major capsid protein VP2 of human parvovirus B19, when studied in a denatured form exhibiting linear epitopes, is recognized exclusively by immunoglobulin G (IgG) antibodies of patients with acute or recent B19 infection. By contrast, conformational epitopes of VP2 are recognized both by IgG of the acute phase and by IgG of past immunity. In order to localize the VP2 linear epitope(s) specific for acute-phase IgG, the entire B19 capsid protein sequence was mapped by peptide scanning using well-characterized acute-phase and control sera. A unique heptapeptide epitope showing strong and sele

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Procyk, R., B. Kudryk, S. Callender, and B. Blomback. "Accessibility of epitopes on fibrin clots and fibrinogen gels." Blood 77, no. 7 (1991): 1469–75. http://dx.doi.org/10.1182/blood.v77.7.1469.1469.

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Abstract Radiolabeled antibodies were perfused into fibrin clots and fibrinogen gels formed in vitro to assess the reactivity of selected epitopes. An antifibrinogen monoclonal antibody (MoAb) (antibody 1D4/xl-f), directed against an epitope in the A alpha-chain C-terminal region (A alpha 241– 476), bound to 35% of the epitope in crosslinked fibrin clots and 37% of the same epitope in factor XIII-induced fibrinogen gel networks. A different MoAb (4–2/xl-f, anti gamma 392–406) bound to only 7% of the epitope in both fibrin and fibrinogen gels. As expected, an antifibrin MoAb (antibody T2G1, ant

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Procyk, R., B. Kudryk, S. Callender, and B. Blomback. "Accessibility of epitopes on fibrin clots and fibrinogen gels." Blood 77, no. 7 (1991): 1469–75. http://dx.doi.org/10.1182/blood.v77.7.1469.bloodjournal7771469.

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Radiolabeled antibodies were perfused into fibrin clots and fibrinogen gels formed in vitro to assess the reactivity of selected epitopes. An antifibrinogen monoclonal antibody (MoAb) (antibody 1D4/xl-f), directed against an epitope in the A alpha-chain C-terminal region (A alpha 241– 476), bound to 35% of the epitope in crosslinked fibrin clots and 37% of the same epitope in factor XIII-induced fibrinogen gel networks. A different MoAb (4–2/xl-f, anti gamma 392–406) bound to only 7% of the epitope in both fibrin and fibrinogen gels. As expected, an antifibrin MoAb (antibody T2G1, antiB beta 1

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Midgley, R. S., A. I. Bell, Q. Y. Yao, et al. "HLA-A11-Restricted Epitope Polymorphism among Epstein-Barr Virus Strains in the Highly HLA-A11-Positive Chinese Population: Incidence and Immunogenicity of Variant Epitope Sequences." Journal of Virology 77, no. 21 (2003): 11507–16. http://dx.doi.org/10.1128/jvi.77.21.11507-11516.2003.

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ABSTRACT An individual's CD8+-cytotoxic-T-lymphocyte (CTL) response to Epstein-Barr virus (EBV) latent cycle antigens focuses on a small number of immunodominant epitopes often presented by just one of the available HLA class I alleles; for example, HLA-A11-positive Caucasians frequently respond to two immunodominant HLA A11 epitopes, IVTDFSVIK (IVT) and AVFDRKSDAK (AVF), within the nuclear antigen EBNA3B. Here, we reexamine the spectrum of EBV strains present in the highly HLA-A11-positive Chinese population for sequence changes in these epitopes relative to the Caucasian type 1 prototype str

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