CDR3αdrives selection of the immunodominant Epstein Barr virus (EBV) BRLF1-specific CD8 T cell receptor repertoire in primary infection.

Larisa Kamga,Dario Ghersi,Anna Gil,Nuray Aslan,Lawrence J Stern,Robin Brody,Katherine Luzuriaga,Liisa K Selin,Inyoung Song,Laurie T Krug

doi:10.1371/journal.ppat.1008122

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.

Highlights

Epstein Barr virus (EBV) infects almost 95 percent of the world’s population by the fourth decade of life
We performed single cell sequencing of paired T cell receptor (TCR) α and β chains from EBV-specific CD8 T cells isolated at two time points from four individuals undergoing acute EBV infection
We describe a TCRα sequence that was shared by all four individuals and identify conserved residues within this sequence that likely contribute to viral recognition

Summary

Introduction

EBV infects almost 95 percent of the world’s population by the fourth decade of life. The TCR is expressed on the surface of the T cell Due to this sequence of events it is not unusual to find T cells with the same TCRβ chain paired with different TCRα; reports of the reverse are, rare. This recombination process results in a diverse pool of unique TCRα and β clonotypes. Additions of non-templated (N) nucleotides or deletions of nucleotides at the V(D)J junctions, commonly known as the complementarity-determining region 3 (CDR3) and pairing of different TCRα and β segments further enhance the overall diversity of the TCR repertoire, estimated to range from 1015−1020 unique potential TCRαβ clonotypes [15, 19]

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