Detection of Enriched T Cell Epitope Specificity in Full T Cell Receptor Sequence Repertoires
| Autor: | Sofie Gielis, Pieter Moris, Wout Bittremieux, Nicolas De Neuter, Benson Ogunjimi, Kris Laukens, Pieter Meysman |
|---|---|
| Přispěvatelé: | Faculty of Arts and Philosophy, Pediatrics |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
T-Cell Antigen Receptor Specificity/genetics T-Lymphocytes Epitopes T-Lymphocyte T-Cell Antigen Receptor Specificity Web Browser immunoinformatics Epitope 0302 clinical medicine Databases Genetic Immunology and Allergy Statistical analysis Original Research Repertoire epitope specificity hemic and immune systems vaccines medicine.anatomical_structure Algorithms TCR repertoire analysis lcsh:Immunologic diseases. Allergy Receptors Antigen T-Cell/genetics T cell infectious disease Immunology Receptors Antigen T-Cell chemical and pharmacologic phenomena Computational biology Biology Models Biological enrichment analysis Clonal Evolution 03 medical and health sciences Antigen medicine Humans Amino Acid Sequence Epitopes T-Lymphocyte/chemistry Epitope specificity Computer. Automation T-cell receptor T-Lymphocytes/immunology Immune state 030104 developmental biology Clonal Evolution/genetics cytomegalovirus (CMV) Human medicine reproducibility of results yellow fever virus (YFV) lcsh:RC581-607 Software 030215 immunology |
| Zdroj: | Frontiers in Immunology, Vol 10 (2019) Frontiers in Immunology Frontiers in immunology |
| ISSN: | 1664-3224 |
| DOI: | 10.3389/fimmu.2019.02820/full |
| Popis: | High-throughput T cell receptor (TCR) sequencing allows the characterization of an individual's TCR repertoire and directly queries their immune state. However, it remains a non-trivial task to couple these sequenced TCRs to their antigenic targets. In this paper, we present a novel strategy to annotate full TCR sequence repertoires with their epitope specificities. The strategy is based on a machine learning algorithm to learn the TCR patterns common to the recognition of a specific epitope. These results are then combined with a statistical analysis to evaluate the occurrence of specific epitope-reactive TCR sequences per epitope in repertoire data. In this manner, we can directly study the capacity of full TCR repertoires to target specific epitopes of the relevant vaccines or pathogens. We demonstrate the usability of this approach on three independent datasets related to vaccine monitoring and infectious disease diagnostics by independently identifying the epitopes that are targeted by the TCR repertoire. The developed method is freely available as a web tool for academic use at tcrex.biodatamining.be. |
| Databáze: | OpenAIRE |
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