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Barra C, Nilsson JB, Saksager A, Carri I, Deleuran S, Garcia Alvarez HM, Høie MH, Li Y, Clifford JN, Wan YTR, Moreta LS, Nielsen M. In Silico Tools for Predicting Novel Epitopes. Methods Mol Biol 2024; 2813:245-280. [PMID: 38888783 DOI: 10.1007/978-1-0716-3890-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Identifying antigens within a pathogen is a critical task to develop effective vaccines and diagnostic methods, as well as understanding the evolution and adaptation to host immune responses. Historically, antigenicity was studied with experiments that evaluate the immune response against selected fragments of pathogens. Using this approach, the scientific community has gathered abundant information regarding which pathogenic fragments are immunogenic. The systematic collection of this data has enabled unraveling many of the fundamental rules underlying the properties defining epitopes and immunogenicity, and has resulted in the creation of a large panel of immunologically relevant predictive (in silico) tools. The development and application of such tools have proven to accelerate the identification of novel epitopes within biomedical applications reducing experimental costs. This chapter introduces some basic concepts about MHC presentation, T cell and B cell epitopes, the experimental efforts to determine those, and focuses on state-of-the-art methods for epitope prediction, highlighting their strengths and limitations, and catering instructions for their rational use.
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Affiliation(s)
- Carolina Barra
- Section for Bioinformatics, Health Tech, Technical University of Denmark, Lyngby, Denmark.
| | | | - Astrid Saksager
- Section for Bioinformatics, Health Tech, Technical University of Denmark, Lyngby, Denmark
| | - Ibel Carri
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Argentina
| | - Sebastian Deleuran
- Section for Bioinformatics, Health Tech, Technical University of Denmark, Lyngby, Denmark
| | - Heli M Garcia Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Argentina
| | - Magnus Haraldson Høie
- Section for Bioinformatics, Health Tech, Technical University of Denmark, Lyngby, Denmark
| | - Yuchen Li
- Section for Bioinformatics, Health Tech, Technical University of Denmark, Lyngby, Denmark
| | | | - Yat-Tsai Richie Wan
- Section for Bioinformatics, Health Tech, Technical University of Denmark, Lyngby, Denmark
| | - Lys Sanz Moreta
- Section for Bioinformatics, Health Tech, Technical University of Denmark, Lyngby, Denmark
| | - Morten Nielsen
- Section for Bioinformatics, Health Tech, Technical University of Denmark, Lyngby, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Argentina
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Beck-García K, Beck-García E, Bohler S, Zorzin C, Sezgin E, Levental I, Alarcón B, Schamel WW. Nanoclusters of the resting T cell antigen receptor (TCR) localize to non-raft domains. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:802-9. [DOI: 10.1016/j.bbamcr.2014.12.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 12/04/2014] [Accepted: 12/15/2014] [Indexed: 10/24/2022]
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N-terminal negatively charged residues in CD3varepsilon chains as a phylogenetically conserved trait potentially yielding isoforms with different isoelectric points: analysis of human CD3varepsilon chains. Immunol Lett 2009; 126:8-15. [PMID: 19616027 DOI: 10.1016/j.imlet.2009.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 06/23/2009] [Accepted: 07/09/2009] [Indexed: 11/21/2022]
Abstract
CD3varepsilon chains are essential to the structure, expression and signaling of T cell receptors. Here, we extend to human CD3varepsilon our previous data in mouse CD3varepsilon showing that, in T cells, proteolytic processing of the acidic N-terminal sequence of CD3varepsilon chains generate distinct polypeptide species that can be identified by two-dimension (IEF-SDS PAGE) electrophoresis and immunoblot. This was shown first by showing the processing of a fusion protein of GFP and the extracellular domain of mouse CD3varepsilon (mCD3GFP) expressed in Jurkat cells. Secondly, pI heterogeneity was also found in human CD3varepsilon chains immunoprecipitated from the surface of Jurkat cells or PHA blasts of human blood T lymphocytes. Comparison of CD3varepsilon chains from 27 different species shows that their N-terminal sequences share a strong acidic nature, despite the large differences in terms of length and composition, even among closely related species. Our results suggest that generation of CD3varepsilon chain isoforms with different N-terminal sequence and pI is a general phenomenon. Thus, as previously observed in the mouse, the relative abundance of CD3varepsilon chain species might regulate TCR/CD3 structure and function, including the strength of the interactions between CD3 dimers and the TCR clonotypic receptors, as well as TCR/CD3 activation thresholds. Interestingly, CD3varepsilon chains from 7 out of 27 species studied have putative N-glycosylation (NxS or NxT) motifs in their Ig extracellular domain. Their location, plus the conservation of residues involved in domain organization, the interactions with other CD3 chains, or the TCR, and signal triggering add new data useful to establish a permissive topology for the interaction between CD3 dimers and the TCR chains.
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Alarcón B, Swamy M, van Santen HM, Schamel WWA. T-cell antigen-receptor stoichiometry: pre-clustering for sensitivity. EMBO Rep 2009; 7:490-5. [PMID: 16670682 PMCID: PMC1479560 DOI: 10.1038/sj.embor.7400682] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Accepted: 03/15/2006] [Indexed: 11/09/2022] Open
Abstract
The T-cell antigen receptor (TCR x CD3) is a multi-subunit complex that is responsible for triggering an adaptive immune response. It shows high specificity and sensitivity, while having a low affinity for the ligand. Furthermore, T cells respond to antigen over a wide concentration range. The stoichiometry and architecture of TCR x CD3 in the membrane have been under intense scrutiny because they might be the key to explaining its paradoxical properties. This review highlights new evidence that TCR x CD3 is found on intact unstimulated T cells in a monovalent form (one ligand-binding site per receptor) as well as in several distinct multivalent forms. This is in contrast to the TCR x CD3 stoichiometries determined by several biochemical means; however, these data can be explained by the effects of different detergents on the integrity of the receptor. Here, we discuss a model in which the multivalent receptors are important for the detection of low concentrations of ligand and therefore confer sensitivity, whereas the co-expressed monovalent TCR x CD3s allow a wide dynamic range.
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MESH Headings
- Animals
- Humans
- Protein Conformation
- Receptor Aggregation/immunology
- Receptor-CD3 Complex, Antigen, T-Cell/chemistry
- Receptor-CD3 Complex, Antigen, T-Cell/metabolism
- Receptor-CD3 Complex, Antigen, T-Cell/physiology
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/physiology
- Signal Transduction/immunology
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Affiliation(s)
- Balbino Alarcón
- Centro de Biología Molecular Severo Ochoa, CSIC-Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Mahima Swamy
- Max Planck-Institut für Immunbiologie and University of Freiburg, Stübeweg 51, 79108 Freiburg, Germany
| | - Hisse M van Santen
- Centro de Biología Molecular Severo Ochoa, CSIC-Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Wolfgang W A Schamel
- Max Planck-Institut für Immunbiologie and University of Freiburg, Stübeweg 51, 79108 Freiburg, Germany
- Tel: +49 761 510 8313; Fax: +49 761 510 8423;
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Wittig I, Schägger H. Features and applications of blue-native and clear-native electrophoresis. Proteomics 2008; 8:3974-90. [DOI: 10.1002/pmic.200800017] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Rossi NE, Reine J, Pineda-Lezamit M, Pulgar M, Meza NW, Swamy M, Risueno R, Schamel WWA, Bonay P, Fernandez-Malave E, Regueiro JR. Differential antibody binding to the surface TCR{middle dot}CD3 complex of CD4+ and CD8+ T lymphocytes is conserved in mammals and associated with differential glycosylation. Int Immunol 2008; 20:1247-58. [DOI: 10.1093/intimm/dxn081] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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The extracellular part of ζ is buried in the T cell antigen receptor complex. Immunol Lett 2008; 116:203-10. [DOI: 10.1016/j.imlet.2007.11.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Revised: 11/27/2007] [Accepted: 11/30/2007] [Indexed: 11/22/2022]
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Swamy M, Dopfer EP, Molnar E, Alarcón B, Schamel WWA. The 450 kDa TCR Complex has a Stoichiometry of alphabetagammaepsilondeltaepsilonzetazeta. Scand J Immunol 2008; 67:418-20; author reply 421. [PMID: 18282230 DOI: 10.1111/j.1365-3083.2008.02082.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Bello R, Feito MJ, Ojeda G, Portolés P, Rojo JM. Loss of N-terminal charged residues of mouse CD3 epsilon chains generates isoforms modulating antigen T cell receptor-mediated signals and T cell receptor-CD3 interactions. J Biol Chem 2007; 282:22324-34. [PMID: 17561508 DOI: 10.1074/jbc.m701875200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The antigen T cell receptor (TCR)-CD3 complexes present on the cell surface of CD4(+) T lymphocytes and T cell lines express CD3 epsilon chain isoforms with different isoelectric points (pI), with important structural and functional consequences. The pI values of the isoforms fit the predicted pI values of CD3 epsilon chains lacking one, two, and three negatively charged amino acid residues present in the N-terminal region. Different T cells have different ratios of CD3 epsilon chain isoforms. At a high pI, degraded CD3 epsilon isoforms can be better recognized by certain anti-CD3 monoclonal antibodies such as YCD3-1, the ability of which to bind to the TCR-CD3 complex is directly correlated with the pI of CD3 epsilon. The abundance of CD3 epsilon isoforms can be modified by treatment of T cells with the proteinase inhibitor phenanthroline. In addition, these CD3 epsilon isoforms have functional importance. This is shown, first, by the different structure of TCR-CD3 complexes in cells possessing different amounts of isoforms (as observed in surface biotinylation experiments), by their different antigen responses, and by the stronger interaction between low pI CD3 epsilon isoforms and the TCR. Second, incubation of cells with phenanthroline diminished the proportion of degraded high pI CD3 epsilon isoforms, but also the ability of the cells to deliver early TCR activation signals. Third, cells expressing mutant CD3 epsilon chains lacking N-terminal acid residues showed facilitated recognition by antibody YCD3-1 and enhanced TCR-mediated activation. Furthermore, the binding avidity of antibody YCD3-1 was different in distinct thymus populations. These results suggest that changes in CD3 epsilon N-terminal chains might help to fine-tune the response of the TCR to its ligands in distinct activation situations or in thymus selection.
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Affiliation(s)
- Raquel Bello
- Departamento de Fisiopatología Celular y Molecular, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, E-28040 Madrid, Spain
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Kuball J, Dossett ML, Wolfl M, Ho WY, Voss RH, Fowler C, Greenberg PD. Facilitating matched pairing and expression of TCR chains introduced into human T cells. Blood 2007; 109:2331-8. [PMID: 17082316 PMCID: PMC1852191 DOI: 10.1182/blood-2006-05-023069] [Citation(s) in RCA: 280] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Accepted: 10/28/2006] [Indexed: 11/20/2022] Open
Abstract
Adoptive transfer of T lymphocytes is a promising treatment for a variety of malignancies but often not feasible due to difficulties generating T cells that are reactive with the targeted antigen from patients. To facilitate rapid generation of cells for therapy, T cells can be programmed with genes encoding the alpha and beta chains of an antigen-specific T-cell receptor (TCR). However, such exogenous alpha and beta chains can potentially assemble as pairs not only with each other but also with endogenous TCR alpha and beta chains, thereby generating alphabetaTCR pairs of unknown specificity as well as reducing the number of exogenous matched alphabetaTCR pairs at the cell surface. We demonstrate that introducing cysteines into the constant region of the alpha and beta chains can promote preferential pairing with each other, increase total surface expression of the introduced TCR chains, and reduce mismatching with endogenous TCR chains. This approach should improve both the efficacy and safety of ongoing efforts to use TCR transfer as a strategy to generate tumor-reactive T cells.
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Affiliation(s)
- Jürgen Kuball
- The Fred Hutchinson Cancer Research Center, Program in Immunology, Seattle, WA 98109, USA.
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Swamy M, Siegers GM, Minguet S, Wollscheid B, Schamel WWA. Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) for the Identification and Analysis of Multiprotein Complexes. Sci Signal 2006; 2006:pl4. [PMID: 16868305 DOI: 10.1126/stke.3452006pl4] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Multiprotein complexes (MPCs) play crucial roles in cell signaling. Two kinds of MPCs can be distinguished: (i) Constitutive, abundant MPCs--for example, multisubunit receptors or transcription factors; and (ii) signal-induced, transient, low copy number MPCs--for example, complexes that form upon binding of Src-homology 2 (SH2) domain-containing proteins to tyrosine-phosphorylated proteins. Blue native polyacrylamide gel electrophoresis (BN-PAGE) is a separation method with a higher resolution than gel filtration or sucrose density ultracentrifugation that can be used to analyze abundant, stable MPCs from 10 kD to 10 MD. In contrast to immunoprecipitation and two-hybrid approaches, it allows the determination of the size, the relative abundance, and the subunit composition of an MPC. In addition, it shows how many different complexes exist that share a common subunit, whether free monomeric forms of individual subunits exist, and whether these parameters change upon cell stimulation. Here, we give a detailed protocol for the separation of MPCs from total cellular lysates or of prepurified MPCs by one-dimensional BN-PAGE or by two-dimensional BN-PAGE and SDS-PAGE.
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Affiliation(s)
- Mahima Swamy
- Max Planck-Institut für Immunbiologie und Universität Freiburg, Biologie III, Stübeweg 51, D-79108 Freiburg, Germany
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