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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 MeysmanEmail author
Protocol
  • 258 Downloads
Part of the Methods in Molecular Biology book series (MIMB, volume 2120)

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.

Key words

TCR repertoire analysis Epitope-specific T cells Immunoinformatics Machine learning TCR repertoire sequencing 

Notes

Acknowledgments

This work was funded by the University of Antwerp with a University Research Fund (BOF Concerted Research Action) and an Industrial Research Fund (IOF), by the Research Foundation Flanders (FWO) [Personal PhD grants to NDN (1S29816N), SG (1S48819N), and PMo (1141217 N); postdoctoral grant to WB (12W0418N); senior clinical investigator grant to BO (1861219 N); and research project grant (G067118 N)], and by the Belgian American Educational Foundation (BAEF) [postdoctoral grant to WB].

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • 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
    • 1
    • 2
    • 3
    Email author
  1. 1.Adrem Data Lab, Department of Mathematics and Computer ScienceUniversity of AntwerpAntwerpBelgium
  2. 2.AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and SequencingUniversity of AntwerpAntwerpBelgium
  3. 3.Biomedical Informatics Research Network Antwerp (biomina), University of AntwerpAntwerpBelgium
  4. 4.Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of CaliforniaSan DiegoUSA
  5. 5.Antwerp Center for Translational Immunology and Virology (ACTIV)Vaccine and Infectious Disease Institute, University of AntwerpAntwerpBelgium
  6. 6.Department of PaediatricsAntwerp University HospitalAntwerpBelgium
  7. 7.Center for Health Economics Research and Modeling Infectious Diseases (CHERMID)Vaccine and Infectious Disease Institute, University of AntwerpAntwerpBelgium

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