Identifying and Tracking Low-Frequency Virus-Specific TCR Clonotypes Using High-Throughput Sequencing

Cell Rep. 2018 Nov 27;25(9):2369-2378.e4. doi: 10.1016/j.celrep.2018.11.009.

Abstract

Tracking antigen-specific T cell responses over time within individuals is difficult because of lack of knowledge of antigen-specific TCR sequences, limitations in sample size, and assay sensitivities. We hypothesized that analyses of high-throughput sequencing of TCR clonotypes could provide functional readouts of individuals' immunological histories. Using high-throughput TCR sequencing, we develop a database of TCRβ sequences from large cohorts of mice before (naive) and after smallpox vaccination. We computationally identify 315 vaccine-associated TCR sequences (VATS) that are used to train a diagnostic classifier that distinguishes naive from vaccinated samples in mice up to 9 months post-vaccination with >99% accuracy. We determine that the VATS library contains virus-responsive TCRs by in vitro expansion assays and virus-specific tetramer sorting. These data outline a platform for advancing our capabilities to identify pathogen-specific TCR sequences, which can be used to identify and quantitate low-frequency pathogen-specific TCR sequences in circulation over time with exceptional sensitivity.

Keywords: DNA sequencing; HLA-A2; T cell receptor; biomarkers; monkeypox; vaccinia.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Cell Tracking*
  • Clone Cells
  • Female
  • Gene Library
  • High-Throughput Nucleotide Sequencing / methods*
  • Male
  • Mice, Inbred C57BL
  • Orthopoxvirus
  • Peptides / chemistry
  • Poxviridae Infections / virology
  • Receptors, Antigen, T-Cell / chemistry
  • Receptors, Antigen, T-Cell / metabolism*
  • Vaccination
  • Viruses / metabolism*

Substances

  • Peptides
  • Receptors, Antigen, T-Cell