Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope

T cell receptor (TCR) sequences are very diverse, with many more possible sequence combinations than T cells in any one individual1–4. Here we define the minimal requirements for TCR antigen specificity, through an analysis of TCR sequences using a panel of peptide and major histocompatibility complex (pMHC)-tetramer-sorted cells and structural data. From this analysis we developed an algorithm that we term GLIPH (grouping of lymphocyte interactions by paratope hotspots) to cluster TCRs with a high probability of sharing specificity owing to both conserved motifs and global similarity of complementarity-determining region 3 (CDR3) sequences. We show that GLIPH can reliably group TCRs of common specificity from different donors, and that conserved CDR3 motifs help to define the TCR clusters that are often contact points with the antigenic peptides. As an independent validation, we analysed 5,711 TCRβ chain sequences from reactive CD4 T cells from 22 individuals with latent Mycobacterium tuberculosis infection. We found 141 TCR specificity groups, including 16 distinct groups containing TCRs from multiple individuals. These TCR groups typically shared HLA alleles, allowing prediction of the likely HLA restriction, and a large number of M. tuberculosis T cell epitopes enabled us to identify pMHC ligands for all five of the groups tested. Mutagenesis and de novo TCR design confirmed that the GLIPH-identified motifs were critical and sufficient for shared-antigen recognition. Thus the GLIPH algorithm can analyse large numbers of TCR sequences and define TCR specificity groups shared by TCRs and individuals, which should greatly accelerate the analysis of T cell responses and expedite the identification of specific ligands.

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“…2a, Extended Data Fig. 4b), which was recently demonstrated in the context of an influenza CD8 + T cell epitope 10 .…”

supporting

confidence: 66%

Identifying specificity groups in the T cell receptor repertoire

Glanville

Huang

Nau

et al. 2017

Nature

807

1,108

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“…To further elucidate factors that are driving selection of TCR specific to the two immunodominant EBV epitopes, the characteristics of the TCR repertoires for each of 3 donors were elucidated by systematically analyzing preferential TCRAV or BV segment usage hierarchy as presented in pie charts, CDR3 length analyses, V-J pairing by Circos plots of the clonotypes with the dominant CDR3 lengths, and dominant CDR3 motif; the last determines if there was an enrichment of particular amino acid residues at specific sites potentially important for ligand interaction. Enrichment for certain characteristics would suggest that these features are important for pMHC interaction (11,29,(47)(48)(49)(50).…”

Section: Resultsmentioning

confidence: 99%

“…Shared TCR␤ amino acid sequences required fewer nucleotide additions and were encoded by a greater variety of nucleotide sequences (i.e., convergent recombination). Both of these features are characteristics of TCR␤ sequences that have the potential to be produced frequently (35)(36)(37)(38)(39) and are also observed in many public TCRs (29,30,(38)(39)(40)(41). To thoroughly evaluate molecular features of TCR that are important for driving repertoire selection over time following EBV infection, we used direct ex vivo deep sequencing of both TCR V␣ and V␤ regions of CD8 T cells specific to two immunodominant epitopes, BRLF-1 109 (YVL-BR) and BMLF-1 280 (GLC-BM), isolated from peripheral blood during primary EBV infection (AIM) and 6 months later in convalescence (CONV).…”

mentioning

confidence: 91%

“…Deep-sequencing techniques, combined with structural analyses, provide a high-throughput and unbiased approach to understanding antigen-specific TCR␣␤ repertoires. We (29) and others (30)(31)(32)(33) have recently reported that TCR␣␤ repertoires of CD8 T cell responses to common viruses (influenza virus, cytomegalovirus [CMV], and hepatitis C virus) are highly diverse and individualized (i.e., "private") but that "public" clonotypes (defined as the same V, J, or CDR3 amino acid sequences in many individuals) are favored for expansion, likely due to selection for optimal structural interactions (34).…”

mentioning

confidence: 99%

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Epstein-Barr Virus Epitope–Major Histocompatibility Complex Interaction Combined with Convergent Recombination Drives Selection of Diverse T Cell Receptor α and β Repertoires

Gil

Kamga

Chirravuri-Venkata

et al. 2020

mBio

Self Cite

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Recognition modes of individual T cell receptors (TCRs) are well studied, but factors driving the selection of TCR repertoires from primary through persistent human virus infections are less well understood. Using deep sequencing, we demonstrate a high degree of diversity of Epstein-Barr virus (EBV)-specific clonotypes in acute infectious mononucleosis (AIM). Only 9% of unique clonotypes detected in AIM persisted into convalescence; the majority (91%) of unique clonotypes detected in AIM were not detected in convalescence and were seeming replaced by equally diverse “de novo” clonotypes. The persistent clonotypes had a greater probability of being generated than nonpersistent clonotypes due to convergence recombination of multiple nucleotide sequences to encode the same amino acid sequence, as well as the use of shorter complementarity-determining regions 3 (CDR3s) with fewer nucleotide additions (i.e., sequences closer to germ line). Moreover, the two most immunodominant HLA-A2-restricted EBV epitopes, BRLF1109 and BMLF1280, show highly distinct antigen-specific public (i.e., shared between individuals) features. In fact, TCRα CDR3 motifs played a dominant role, while TCRβ played a minimal role, in the selection of TCR repertoire to an immunodominant EBV epitope, BRLF1. This contrasts with the majority of previously reported repertoires, which appear to be selected either on TCRβ CDR3 interactions with peptide/major histocompatibility complex (MHC) or in combination with TCRα CDR3. Understanding of how TCR-peptide-MHC complex interactions drive repertoire selection can be used to develop optimal strategies for vaccine design or generation of appropriate adoptive immunotherapies for viral infections in transplant settings or for cancer. IMPORTANCE Several lines of evidence suggest that TCRα and TCRβ repertoires play a role in disease outcomes and treatment strategies during viral infections in transplant patients and in cancer and autoimmune disease therapy. Our data suggest that it is essential that we understand the basic principles of how to drive optimum repertoires for both TCR chains, α and β. We address this important issue by characterizing the CD8 TCR repertoire to a common persistent human viral infection (EBV), which is controlled by appropriate CD8 T cell responses. The ultimate goal would be to determine if the individuals who are infected asymptomatically develop a different TCR repertoire than those that develop the immunopathology of AIM. Here, we begin by doing an in-depth characterization of both CD8 T cell TCRα and TCRβ repertoires to two immunodominant EBV epitopes over the course of AIM, identifying potential factors that may be driving their selection.

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“…In this scenario, flu responses, generally more specifically driven by CDR3 contacts 47,56 as most usual epitopes, could occasionally amplify a rare TCR heterodimer containing CDR3 TRBV15 CATSRDTMTSIGTDTQYF, TRBV4−2 CASSQETQGRNYGYTF, TRBV4-3 CASSQGNTGHSPLHF or TRBV4-3 CASSQGDVNYGYTF coupled with TRAV2 CAVETDSWGKLQF TRAJ24 (nodes connecting pHA273-287 and HCRTNH2 networks in Figure 4b), inducing autoimmunity via cross-reactivity to HCRTNH2. Table 6).…”

Section: Discussionmentioning

confidence: 99%