INTRODUCTION
The diversity and functionality of CD8+ T cells recruited during an epitope-specific response is thought to arise through the contribution of antigen density1, antigen sensitivity2, TCR gene biases3, and other factors, but the precise contributions are incompletely understood. There are further constraints which shape the diversity of the final repertoire based on structural features at key conserved residues4 and consideration of a T-cell clone’s pre-existing frequency in the naïve repertoire5,6although this may be overcome by repeated antigen re-exposure through vaccination7. Typically, these factors conspire to generate epitope-specific responses consisting of a range of unique TCR arrangements (clonotypes)8, with a distinct affinity for their cognate peptide in the context of MHC (pMHC). Notably however, epitope-specific populations have been observed to comprise few or single unique clonotypes during infection with human immunodeficiency virus9 and Mycobacterium tuberculosis 10. Such monoclonal populations may have arisen through a selective advantage intrinsically conferred by its specific TCR clonotype.
The affinity of the TCR-pMHC interaction may be measured by both its association (kon) and dissociation (koff) constants, which collectively contribute to its host cell’s activation potency11. One such method for the measurement of the koff rate utilises dissociable HLA multimers, so-called MHC Streptamers, which allow the real-time tracking of dissociation of monomeric TCR-pMHC complexes by flow cytometry12-14. Notably, CD8+ T cell clonotypes with lower koff constants (or practically, high-affinity clones with extended dissociation times) have improved protective capacity when used for adoptive transfer13and high affinity neoantigen-specific clones are more effective at slowing tumor growth15. By contrast, low-affinity clonotypes are preferentially expanded long-term during chronic cytomegalovirus infection16, may be better suited for providing responses optimised against antigens with relatively higher abundance17, and provide the flexibility for recognising and responding to mutated epitopes18. Taken together, these studies provide evidence that the affinity of TCR-pMHC interactions likely influence the functional capacity of epitope-specific populations.
In this study, we characterised the phenotype and affinity of a naturally-derived monoclonal CD8+ T cell population arising from an individual with acutely resolving infection that we had reported on previously19. We examined three hepatitis C virus (HCV)-specific CD8+ T cell populations from two individuals and profiled each population’s respective repertoire diversity, phenotypic characteristics, and dissociation affinities at the single-cell level. The koff rate-derived affinity of the monoclonal TCR clonotype was the strongest out of all tested sequences, although clonotypes from a polyclonal population targeting the same epitope also displayed surprisingly strong affinities. Notably, analysis of the transcriptional signatures from each population revealed associations between epitope specificity, affinity and molecular phenotype. Our findings contribute to an improved understanding of the heterogeneity of TCR repertoires generated by viral infections and offer insights into how affinity may shape the phenotype and expansion of T cells at the epitope-specific level.