TCRαβ repertoire plasticity defines universal CD8+ T cell responses directed at influenza-specific HLA-A*02:01-PB1413-421 epitope

HLA-A*02:01-restricted PB1413+CD8+ T cells provide the broadest reported cross-reactive immunity against influenza A, B, and C viruses. Here, we investigated T cell receptor (TCR) clonotypic signatures within these universal A2/PB1413+CD8+ T cell pools, compared with immunodominant influenza A-specific M158+CD8+ T cells and codominant influenza B-specific A2/HA543+CD8+ memory T cells. Using single-cell reverse transcriptase polymerase chain reaction and RNA sequencing methodologies, we defined TCRαβ repertoire composition and diversity. Our study shows that CD8+ T cells responding to these 3 epitopes differ in magnitude and TCRαβ repertoires in terms of gene usage and sharing, underpinned by specific TCR and structural features for each pMHC-I specificity. Our data demonstrated that the A2/PB1413+CD8+ TCRαβ repertoire encompassed diverse gene segment usage within both TCRα and TCRβ chains. These were, however, greatly variable across HLA-A2*02:01-expressing individuals and lacked any shared features within TRAV, TRBV, TRBJ, and TRAJ gene segments. This A2/PB1413+CD8+ TCRαβ diversity stemmed from the low probability of recombination attributed to a large number of N-insertions in the TCRβ chain. PB1413+CD8+ T cells also displayed remarkable plasticity in recognition of the A2/PB1413 epitope depicted by versatile CD8+ T cell recognition patterns of the universal A2/PB1413 epitope across HLA-A*02:01-expressing individuals. Conversely, TCRαβ repertoires within A2/BHA543+CD8+ and M158+CD8+ T cells displayed common TRAV, TRBV, TRBJ, and TRAJ gene segments, shared across HLA-A*02:01-expressing individuals and recognizing key residues within A2/BHA543 and A2/M158 epitopes. Overall, our data showed a great level of TCRαβ gene usage diversity within universal A2/PB1413+CD8+ T cells, indicating that the TCRαβ clonal plasticity defines universal immunity toward human influenza viruses.