Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence

Abstract

Motivation: The clonal theory of adaptive immunity proposes that immunological responses are encoded by increases in the frequency of lymphocytes carrying antigen-specific receptors. In this study, we measure the frequency of different T-cell receptors (TcR) in CD4 + T cell populations of mice immunized with a complex antigen, killed Mycobacterium tuberculosis, using high throughput parallel sequencing of the TcRβ chain. Our initial hypothesis that immunization would induce repertoire convergence proved to be incorrect, and therefore an alternative approach was developed that allows accurate stratification of TcR repertoires and provides novel insights into the nature of CD4 + T-cell receptor recognition.Results: To track the changes induced by immunization within this heterogeneous repertoire, the sequence data were classified by counting the frequency of different clusters of short (3 or 4) continuous stretches of amino acids within the antigen binding complementarity determining region 3 (CDR3) repertoire of different mice. Both unsupervised (hierarchical clustering) and supervised (support vector machine) analyses of these different distributions of sequence clusters differentiated between immunized and unimmunized mice with 100% efficiency. The CD4 + TcR repertoires of mice 5 and 14 days postimmunization were clearly different from that of unimmunized mice but were not distinguishable from each other. However, the repertoires of mice 60 days postimmunization were distinct both from naive mice and the day 5/14 animals. Our results reinforce the remarkable diversity of the TcR repertoire, resulting in many diverse private TcRs contributing to the T-cell response even in genetically identical mice responding to the same antigen. However, specific motifs defined by short stretches of amino acids within the CDR3 region may determine TcR specificity and define a new approach to TcR sequence classification.Availability and implementation: The analysis was implemented in R and Python, and source code can be found in Supplementary Data.Contact: b.chain@ucl.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.

Specificity, Privacy, and Degeneracy in the CD4 T Cell Receptor Repertoire Following Immunization

“…We have previously used short read parallel HTS to estimate T cell receptor β transcript frequencies and sharing (14, 15), and to explore the global changes in the CD4+ T cell receptor repertoire following immunization (16). The latter study focused on local features of protein sequence within the TCRβ CDR3 loop, which interacts directly with peptide antigen lying within the MHC groove.…”

A high density of tertiary lymphoid structure B cells in lung tumors is associated with increased CD4+T cell receptor repertoire clonality

“…1 This large repertoire of T or B cell receptors (TCRs or BCRs, respectively), generated by random rearrangements of the variable (V), diversity (D), and joining (J) segments during haematopoesis, is intentionally diverse for generalized targeting of a broad range of potential antigens. [1][2][3] Following binding of the TCR or BCR to its cognate antigen, na€ ıve T or B lymphocytes become activated, proliferate and may undergo somatic mutations of the V regions to improve the binding affinity of the TCR and BCR to antigen as well as class switch recombination. 4,5 Clonal expansion (i.e., high clonality), or the large increase in T or B cells from a single cell, can be the interpreted as the opposite of diversity -the latter of which indicates a variety of different clones with few dominant clones at high frequencies.…”

“…2 As humans age, immune responses become impaired, characterized by (1) reduced lymphopoiesis of new na€ ıve B and T cells, with novel BCRs 6 and TCRs, 7 respectively, (2) reduced dendritic cell (DC) function resulting in poor responses to inflammatory signals and lowered capacity to present antigen and to activate adaptive immune responses, 8 (3) poor germinal center formation, site of B cell expansion and selection, 9 and (4) decreased potential for T cell expansion, expression of activation markers, production of cytokines, diversity of TCR repertoire and delayed T cell responses to antigen. 7,10 Thus, these changes during aging help to explain the increased susceptibility to infection and reduced response to vaccinations in the elderly population.…”

“…[17][18][19][20] Primers specific for the V, D, J, and constant (C) gene segments of the complementarity-determining region 3 (CDR3) of TCRs and BCRs are used to generate millions of sequencing reads and thousands of unique clonotypes, with distributional properties that can be monitored over time or compared between the tumor or normal tissue compartments within a cancer patient. The CDR3 region of the receptor is the primary CDR that contributes most to the antigen recognition by the interaction between the TCR and its cognate peptide antigen located within the major histocompatibility complex groove, or BCR with its cognate polypeptide antigen, 2,21 and is the principle component of antigen recognition specificity in both TCRs and BCRs. 22 TCR and BCR repertoire technology can provide a robust characterization of the global receptor repertoire of particular lymphocyte populations, though within both the peripheral and diseaseaffected compartments, there is a mixed population of T cells that can differ by clonotype contribution, cell subtypes, and sensitivities to therapies.…”

“…22 TCR and BCR repertoire technology can provide a robust characterization of the global receptor repertoire of particular lymphocyte populations, though within both the peripheral and diseaseaffected compartments, there is a mixed population of T cells that can differ by clonotype contribution, cell subtypes, and sensitivities to therapies. 2,3,23 Further, the frequencies of monoclonal and oligoclonal TCR Vb families have been shown to significantly differ between CD4…”