CDR3α drives selection of the immunodominant Epstein Barr virus (EBV) BRLF1-specific CD8 T cell receptor repertoire in primary infection

PLoS Pathog. 2019 Nov 25;15(11):e1008122. doi: 10.1371/journal.ppat.1008122. eCollection 2019 Nov.

Abstract

The T cell receptor (TCR) repertoire is an essential component of the CD8 T-cell immune response. Here, we seek to investigate factors that drive selection of TCR repertoires specific to the HLA-A2-restricted immunodominant epitope BRLF1109-117 (YVLDHLIVV) over the course of primary Epstein Barr virus (EBV) infection. Using single-cell paired TCRαβ sequencing of tetramer sorted CD8 T cells ex vivo, we show at the clonal level that recognition of the HLA-A2-restricted BRLF1 (YVL-BR, BRLF-1109) epitope is mainly driven by the TCRα chain. For the first time, we identify a CDR3α (complementarity determining region 3 α) motif, KDTDKL, resulting from an obligate AV8.1-AJ34 pairing that was shared by all four individuals studied. This observation coupled with the fact that this public AV8.1-KDTDKL-AJ34 TCR pairs with multiple different TCRβ chains within the same donor (median 4; range: 1-9), suggests that there are some unique structural features of the interaction between the YVL-BR/MHC and the AV8.1-KDTDKL-AJ34 TCR that leads to this high level of selection. Newly developed TCR motif algorithms identified a lysine at position 1 of the CDR3α motif that is highly conserved and likely important for antigen recognition. Crystal structure analysis of the YVL-BR/HLA-A2 complex revealed that the MHC-bound peptide bulges at position 4, exposing a negatively charged aspartic acid that may interact with the positively charged lysine of CDR3α. TCR cloning and site-directed mutagenesis of the CDR3α lysine ablated YVL-BR-tetramer staining and substantially reduced CD69 upregulation on TCR mutant-transduced cells following antigen-specific stimulation. Reduced activation of T cells expressing this CDR3 motif was also observed following exposure to mutated (D4A) peptide. In summary, we show that a highly public TCR repertoire to an immunodominant epitope of a common human virus is almost completely selected on the basis of CDR3α and provide a likely structural basis for the selection. These studies emphasize the importance of examining TCRα, as well as TCRβ, in understanding the CD8 T cell receptor repertoire.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • CD8-Positive T-Lymphocytes / immunology*
  • Complementarity Determining Regions / genetics
  • Complementarity Determining Regions / immunology*
  • Complementarity Determining Regions / metabolism
  • Epitopes, T-Lymphocyte / immunology
  • Epstein-Barr Virus Infections / immunology*
  • Epstein-Barr Virus Infections / virology
  • HLA-A2 Antigen / immunology
  • Herpesvirus 4, Human / immunology*
  • Humans
  • Immediate-Early Proteins / genetics
  • Immediate-Early Proteins / immunology*
  • Immediate-Early Proteins / metabolism
  • Immunodominant Epitopes / immunology*
  • Peptide Fragments / immunology
  • Receptors, Antigen, T-Cell, alpha-beta / genetics
  • Receptors, Antigen, T-Cell, alpha-beta / immunology*
  • Receptors, Antigen, T-Cell, alpha-beta / metabolism
  • T-Lymphocytes, Cytotoxic / immunology*
  • Trans-Activators / genetics
  • Trans-Activators / immunology*
  • Trans-Activators / metabolism

Substances

  • BRLF1 protein, Human herpesvirus 4
  • Complementarity Determining Regions
  • Epitopes, T-Lymphocyte
  • HLA-A2 Antigen
  • Immediate-Early Proteins
  • Immunodominant Epitopes
  • Peptide Fragments
  • Receptors, Antigen, T-Cell, alpha-beta
  • Trans-Activators