T Cell Receptor Repertoire Analysis Reveals Signatures of T Cell Responses to Human Mycobacterium tuberculosis

Characterization of T cell receptor (TCR) repertoires is essential for understanding the mechanisms of Mycobacterium tuberculosis (Mtb) infection involving T cell adaptive immunity. The characteristics of TCR sequences and distinctive signatures of T cell subsets in tuberculous patients are still unclear. By combining single-cell TCR sequencing (sc-TCR seq) with single-cell RNA sequencing (sc-RNA seq) and flow cytometry to characterize T cells in tuberculous pleural effusions (TPEs), we identified 41,718 CD3(+) T cells in TPEs and paired blood samples, including 30,515 CD4(+) T cells and 11,203 CD8(+) T cells. Compared with controls, no differences in length and profile of length distribution were observed in complementarity determining region 3 (CDR3) in both CD4(+) and CD8(+) T cells in TPE. Altered hydrophobicity was demonstrated in CDR3 in CD8(+) T cells and a significant imbalance in the TCR usage pattern of T cells with preferential expression of TRBV4-1 in TPE. A significant increase in clonality was observed in TCR repertoires in CD4(+) T cells, but not in CD8(+) T cells, although both enriched CD4(+) and CD8(+) T cells showed T(H)1 and cytotoxic signatures. Furthermore, we identified a new subset of polyfunctional CD4(+) T cells with CD1-restricted, T(H)1, and cytotoxic characteristics, and this subset might provide protective immunity against Mtb.