Antigen specificity, not tissue compartment, determines clonal sharing among respiratory tract CD8⁺ resident memory T cells.

Tissue-resident memory (Trm) CD8⁺ T cells in the upper and lower respiratory tract play an instrumental role in combatting influenza virus. While CD8⁺ Trm populations in these compartments differ in longevity and developmental requirements, it remains unclear whether they share clonotypes, indicating a common origin, or are seeded by distinct T-cell clones. Using a mouse model of influenza virus infection, we investigated the T-cell receptor (TCR) composition of CD8⁺ Trm specific for two immunodominant influenza-specific CD8⁺ T-cell epitopes, derived from the nucleoprotein (NP₃₆₆₋₃₇₄) and polymerase acidic protein (PA₂₂₄₋₂₃₃). TCRαβ repertoire analysis of NP₃₆₆₋₃₇₄-specific CD8⁺ T cells from the nasal mucosa, lung and spleen revealed substantial clonal overlap across resident and circulating subsets, consistent with derivation from a shared precursor pool. In contrast, PA₂₂₄₋₂₃₃-specific responses showed minimal clonal sharing across tissues and subsets, reflecting a more diverse and private repertoire. Thus, nasal and lung CD8⁺ Trm can arise from either shared or distinct clonotypes, with their profiles shaped primarily by the antigen specificity rather than tissue location. This allows barrier tissues to be seeded by both highly conserved, public NP₃₆₆₋₃₇₄-specific CD8⁺ TCRs and a more diverse, private PA₂₂₄₋₂₃₃-specific repertoire, together forming an optimal pool capable of providing broadly cross-reactive T-cell immunity and limiting viral escape.