Ecological analysis of antigen-specific CTL repertoires defines the relationship between naïve and immune T-cell populations

Abstract

Ecology is typically thought of as the study of interactions organisms have with each other and their environment and is focused on the distribution and abundance of organisms both within and between environments. On a molecular level, the capacity to probe analogous questions in the field of T-cell immunology is imperative as we acquire substantial datasets both on epitope-specific T-cell populations through high-resolution analyses of T-cell receptor (TCR) use and on global T-cell populations analyzed via high-throughput DNA sequencing. Here, we present the innovative application of existing statistical measures (used typically in the field of ecology), together with unique statistical analyses, to comprehensively assess how the naïve epitope-specific CD8 + cytotoxic T lymphocyte (CTL) repertoire translates to that found following an influenza-virus-specific immune response. Such interrogation of our extensive, cumulated TCR CDR3β sequence datasets, derived from both naïve and immune 114 , and influenza nonstructural protein 2 amino acid residues 114-121), demonstrates that epitope-specific TCR use in an antiviral immune response is the consequence of a complex interplay between the intrinsic characteristics of the naïve cytotoxic T lymphocyte precursor pool and extrinsic (likely antigen driven) influences, the contribution of which varies in an epitopespecific fashion.+ cytotoxic T lymphocytes (CTLs), the clonotypic T-cell receptor (TCR) recognizes "nonself" peptides (p) in complex with "self" class I MHC glycoproteins (MHCI). To recognize and respond to the vast array of novel pMHCI determinants encountered by a given individual (or population), the adaptive immune system uses the recombination of variable (V), junctional (J), diversity (D), and constant (C) somatic gene segments to establish an extraordinary spectrum of TCRs. Most of the observed TCR diversity results from imprecise joining of these gene segments and the addition of nontemplate-encoded nucleotides at V(D)J junctions (1). The consequence is that TCR diversity is principally a function of the CDR3 regions, meaning that clonal uniqueness is reliably defined by the TCRαβ CDR3 sequences.The nature of the highly specific TCR-pMHC recognition event likely determines functional outcomes after T-cell activation (2-6). Thus, the complexity and distribution of TCR use within a responding CTL population is likely to have a very real impact on the efficacy of T-cell-mediated pathogen clearance. Certainly, both virus control and the prevention of mutational escape operate more effectively if the host response is characterized by a diverse, rather than a limited, spectrum of pMHCI-specific TCRs (7-12). Further, TCR diversity has also been associated with effective cross-reactive immunity against different virus infections (13).Single cell RT-PCR analysis of CDR3 nucleotide sequences has provided an unprecedented level of resolution for characterizing TCR use, especially in the case of CTL responses to pathogens. Such detailed dissection of epitope-speci...

Reproducible selection of high avidity CD8 + T-cell clones following secondary acute virus infection

“…Overall, there was no statistically significant change in clonal diversity (P = 0.45). Similar results were obtained when analysis was restricted to evenness of clonal distribution using the Gini coefficient (21,23) (Fig. S5).…”

“…Fig. 5 shows Simpson's diversity index (SDI; a function of clone number and distribution) values (20)(21)(22) for the TCRβ repertoires analyzed at the indicated stages, with related repertoires connected. Of the 20 repertoires analyzed in the acute recall response (those shown in Table S1 and three recipients from experiment in Fig.…”

The Influenza Virus–Specific CTL Immunodominance Hierarchy in Mice Is Determined by the Relative Frequency of High-Avidity T Cells

“…Although we have previously shown selective expansion of T cells from the naive into the immune repertoire (17,28), the data in this study suggest that this selection favors high-avidity T cells. Intriguingly, the proportion of high-avidity cells in both the naive and immune populations for all of the epitope specificities analyzed reflected the immunodominance hierarchy observed postinfection, with NP 366 -and PA 224 -specific populations containing significantly more high-avidity cells than the PB1-F2 62 or NS2 114 populations (p , 0.001).…”

MHC-derived allopeptide activates TCR-biased CD8+ Tregs and suppresses organ rejection

“…However, interindividually shared TCR sequences are not necessarily dominant in the immune response to antigen (47). This appears to be the case in our model, suggesting that this process may be modified by either TCR expansion or TCRα chain pairing.…”