TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors.
Chronister, W. D., Crinklaw, A., Mahajan, S., Vita, R., Kosaloglu-Yalcin, Z., Yan, Z., Greenbaum, J. A., Jessen, L. E., Nielsen, M., Christley, S., Cowell, L. G., Sette, A. and Peters, B.
La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.
Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark.
Instituto de Investigaciones Biotecnologicas, Universidad Nacional de San Martin, San Martin, Argentina.
Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, United States.
Department of Medicine, University of California, San Diego, San Diego, CA, United States.
The adaptive immune system in vertebrates has evolved to recognize non-self antigens, such as proteins expressed by infectious agents and mutated cancer cells. T cells play an important role in antigen recognition by expressing a diverse repertoire of antigen-specific receptors, which bind epitopes to mount targeted immune responses. Recent advances in high-throughput sequencing have enabled the routine generation of T-cell receptor (TCR) repertoire data. Identifying the specific epitopes targeted by different TCRs in these data would be valuable. To accomplish that, we took advantage of the ever-increasing number of TCRs with known epitope specificity curated in the Immune Epitope Database (IEDB) since 2004. We compared seven metrics of sequence similarity to determine their power to predict if two TCRs have the same epitope specificity. We found that a comprehensive k-mer matching approach produced the best results, which we have implemented into TCRMatch, an openly accessible tool (http://tools.iedb.org/tcrmatch/) that takes TCR beta-chain CDR3 sequences as an input, identifies TCRs with a match in the IEDB, and reports the specificity of each match. We anticipate that this tool will provide new insights into T cell responses captured in receptor repertoire and single cell sequencing experiments and will facilitate the development of new strategies for monitoring and treatment of infectious, allergic, and autoimmune diseases, as well as cancer.
Frontiers in Immunology 12: 640725 (2021)