Single-Cell TCR Sequencing Reveals the Dynamics of T Cell Repertoire Profiling During Pneumocystis Infection

Abstract

T cell responses play critical roles in host adaptive immunity against <i>Pneumocystis</i>. However, the dynamics and diversity of the T cell immune repertoire in human immunodeficiency virus (HIV)-negative <i>Pneumocystis</i> pneumonia (PCP) remains unclear. In this study, single-cell RNA and single-cell T cell receptor (TCR) sequencing were applied to cells sorted from lung tissues of mice infected with <i>Pneumocystis</i>. Our findings demonstrated the clonal cells were mainly composed of CD4⁺ T cells in response to <i>Pneumocystis</i>, which were marked by highly expressed genes associated with T cell activation. Mice infected with <i>Pneumocystis</i> showed reduced TCR diversity in CD4⁺ T cells and increased diversity in CD8⁺ T cells compared with uninfected controls. Furthermore, Th17 cells were mostly clonal CD4⁺ T cells, which exhibited the phenotype of tissue-resident memory-like Th17 cells. In addition, <i>Pneumocystis</i>-infected mice showed biased usage of TCRβ VDJ genes. Taken together, we characterized the transcriptome and TCR immune repertoires profiles of expanded T cell clones, which demonstrate a skewed TCR repertoire after <i>Pneumocystis</i> infection.