High rates of cross-reactivity among apparently unrelated specificities shape antigen-specific T cell receptor repertoires

We have analyzed several thousand antigen-specific T cell receptor repertoires from multiple animals infected with influenza virus and/or murine cytomegalovirus (mCMV). Insights into the overall structure of antigen-specific repertoire landscapes towards 7 different specificities were generated from single cell paired TCR αβ sequencing. In addition to characterization of repertoire features such as diversity, clonal structure, convergent recombination, and key deterministic features of antigen-specificity, we observed a surprisingly high rate of single or dual chain sharing between otherwise unrelated responses. These shared receptors were often observed across multiple animals in independent experiments. However, sharing appeared more likely to occur in animals where the two epitopes were presented simultaneously. Cloning and expression of these unique specificities has allowed further receptor characterization. Additional data indicate that some combinations of co-presented epitopes result in broader repertoires recruited to one or both epitopes. In summary, T cell receptors have a significant propensity for cross-reactivity across otherwise unrelated specificities, an effect that appears to be driven by co-presentation and substantially shapes the magnitude and diversity of antigen-specific repertoires.