Clonotypic Insulation And Microbiome-Associated Filtering Define The Human Airway T Cell Repertoire

Adaptive immune responses are distributed across anatomically distinct compartments of the human respiratory tract, yet comparative characterization of transcriptome-derived T-cell receptor (TCR) repertoires across these compartments remains limited. Here, we reconstructed transcriptome-derived T-cell receptor repertoires from bulk RNA-seq using TRUST4 to compare peripheral blood (n = 24), bronchoalveolar lavage (BAL; n = 55), and induced sputum (n = 100) from a well-characterized rural Ugandan cohort comprising individuals with and without HIV infection and chronic obstructive pulmonary disease (COPD). Comparative analyses revealed marked differences in productive TCR recovery, clonotype richness, diversity, and clonotype sharing across anatomical compartments, with induced sputum yielding fewer reconstructed clonotypes than BAL and peripheral blood despite comparable sequencing depth. In contrast, TRBV gene usage, CDR3 length distributions, amino acid composition, and global TRB sequence-space organization were broadly conserved. Together, these findings establish a comparative reference framework for transcriptome-derived TCR repertoire analysis across peripheral blood and the human respiratory tract.