Identification of Epitope-Specific T Cells in T-Cell Receptor Repertoires

Sofie Gielis; Pieter Moris; Wout Bittremieux; Nicolas De Neuter; Benson Ogunjimi; Kris Laukens; Pieter Meysman

doi:10.1007/978-1-0716-0327-7_13

Identification of Epitope-Specific T Cells in T-Cell Receptor Repertoires

Methods Mol Biol. 2020:2120:183-195. doi: 10.1007/978-1-0716-0327-7_13.

Authors

Sofie Gielis^{1

2

3}, Pieter Moris^{1

3}, Wout Bittremieux^{1

3

4}, Nicolas De Neuter^{1

2

3}, Benson Ogunjimi^{2

5

6

7}, Kris Laukens^{1

2

3}, Pieter Meysman^{8

9

10}

Affiliations

¹ Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.
² AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.
³ Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium.
⁴ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA.
⁵ Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
⁶ Department of Paediatrics, Antwerp University Hospital, Antwerp, Belgium.
⁷ Center for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
⁸ Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium. [email protected].
⁹ AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium. [email protected].
¹⁰ Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium. [email protected].

PMID: 32124320
DOI: 10.1007/978-1-0716-0327-7_13

Abstract

Recognition of cancer epitopes by T cells is fundamental for the activation of targeted antitumor responses. As such, the identification and study of epitope-specific T cells has been instrumental in our understanding of cancer immunology and the development of personalized immunotherapies. To facilitate the study of T-cell epitope specificity, we developed a prediction tool, TCRex, that can identify epitope-specific T-cell receptors (TCRs) directly from TCR repertoire data and perform epitope-specificity enrichment analyses. This chapter details the use of the TCRex web tool.

Keywords: Epitope-specific T cells; Immunoinformatics; Machine learning; TCR repertoire analysis; TCR repertoire sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Epitopes, T-Lymphocyte / immunology*
Humans
Machine Learning
Models, Immunological
Receptors, Antigen, T-Cell / immunology*
Software
T-Cell Antigen Receptor Specificity
T-Lymphocytes / immunology*

Substances

Epitopes, T-Lymphocyte
Receptors, Antigen, T-Cell