Sequence and structural analyses reveal distinct and highly diverse human CD8+ TCR repertoires to immunodominant viral antigens

Abstract A diverse TCR repertoire is considered as an essential property of T cell immunity to efficiently contain and eliminate viral invasion. However, limited information is available regarding the characteristics of TCR repertoire to a defined viral antigen peptide in human. Here, we report a comprehensive analysis of CD8 TCR repertoires, consensus binding motifs in CDR3, affinities of selected TCR/pMHCs, and crystal structures of two dominant viral antigens (CMV pp65-NLV and IAV M1-GIL) from 8 healthy adults. A few thousands of distinct TCR alpha and beta chains for NLV and GIL were identified containing highly selected public TCRs. The repertoire of NLV-specific TCR was substantially more diverse than that of GIL-specific TCR for both alpha and beta chains. Further analysis of CDR3 amino acid sequences revealed dozens of distinct consensus motifs in alpha and beta chains of both antigen specific TCRs. Single cell analysis showed preference of the CDR3 motifs paring between TCR alpha and beta. The affinity of TCR/pMHC ranged more widely for GIL (Kd, 1.8–191 μM) than for NLV (4.7–28 μM). Structural analysis exhibited similar patterns of three TCR-GIL-HLA-A2 interactions, while two distinct binding patterns among three TCR-NLV-HLA-A2 interactions. Our findings revealed highly diverse viral antigen-specific CD8 TCR repertoire, the consensus binding motifs in CDR3, binding affinity of TCR and pMHC, and different patterns of TCR-pMHC interactions. Such information will be essential to understand the make-up of T cell immunity and to guide the potential immune based clinical intervention such as cell therapy.