Stable global repertoire architecture masks short-term clonal remodeling in intratumoral TCR repertoires

Background Tumor-infiltrating T cell receptor repertoires are increasingly profiled to assess intratumoral T cell dynamics and inform prognosis and treatment response. Most analyzes rely on aggregate diversity metrics, such as Shannon index or clonality, which describe overall repertoire structure but do not resolve changes in clonotype identity over time. Thus, intrinsic temporal dynamics of intratumoral T cell receptor repertoires during tumor progression remain incompletely defined. Methods In a bilateral murine cancer model, one tumor was surgically removed, and the paired tumor was collected 11 days later. The T cell receptor repertoires of these tumors, and of synchronously harvested bilateral tumors from separate control animals, were analyzed using diversity metrics, Morisita–Horn similarity, and clonal tracking approaches. Results Time-matched bilateral tumors exhibited highly similar clonotype composition and abundance. In contrast, time-separated tumors showed reduced clonal overlap, increased fractions of private clonotypes, and redistribution of dominant clones. These changes occurred despite preserved global repertoire metrics, including clonotype number, Shannon diversity, and Gini coefficient. Conclusion Short-term tumor progression is associated with clear changes in the composition of the intratumoral T cell receptor repertoire, even when overall diversity appears stable. These results suggest that relying solely on global diversity metrics can obscure active clonal remodeling, underscoring the importance of monitoring individual T cell clonotypes to accurately capture intratumoral T cell dynamics over time.