Single-cell transcriptomics reveal PD-1-loss-driven immune dysregulation of pulmonary lymphocytes during early <i>Mycobacterium tuberculosis</i> infection

ABSTRACT Although PD-1 blockade shows strong antitumor efficacy and is being considered for chronic infections including Mycobacterium tuberculosis ( M.tb ), its influence on early lymphocyte responses to M.tb remains poorly understood. In this study, we characterized the transcriptional and developmental states of pulmonary B and T cells in mice lacking PD-1 after 7 days post- M.tb infection. We found that loss of PD-1 disturbed pulmonary lymphocyte homeostasis, characterized by abnormal regulatory T cell (Tregs) expansion, early exhaustion-like differentiation of cytotoxic T cells, and impaired maturation of memory B cells. These alterations are associated with changes in key transcriptional regulators, including reduced activity of factors promoting effector differentiation (e.g., Runx2 , Runx3 in T cells; Tcf4 , Pou2f2 in B cells) and upregulation of regulators driving regulatory or suppressive phenotypes (e.g., Ikzf2 in Tregs). Additionally, PD-1 deficiency rewired B-T cell communication with diminished antigen presentation and co-stimulation while amplifying proinflammatory signals. These insights provide a transcriptional blueprint for PD-1-mediated immune balance, with implications for host-directed therapies in tuberculosis . IMPORTANCE While PD-1 inhibition can boost protective T cell responses, it has also been linked to increased TB susceptibility. Our study reveals that PD-1 plays a previously unrecognized role in shaping the earliest immune responses to M.tb . In mice lacking PD-1, lung lymphocytes failed to develop in a balanced manner: regulatory T cells expanded excessively, cytotoxic T cells showed signs of early exhaustion, and memory B cell maturation was delayed. These changes disrupted the normal communication between B and T cells, weakening adaptive immunity while amplifying inflammation. By defining PD-1 as a critical organizer of early lymphocyte fate, our findings highlight the risks of indiscriminate PD-1 blockade in infectious contexts and point toward more precise strategies for host-directed TB therapies and vaccine design.