PD-1 genetic fate mapping uncovers immune cell diversity mediating the efficacy of combined PD-1 blockade and chemotherapy.

Combined cytotoxic chemotherapy and immune checkpoint inhibition (ICI) improves outcomes in PD-L1-low lung cancer, but transient and broad PD-1 expression across immune cells complicates the understanding of the underlying mechanisms. We generated Pdcd1-CreERT2 fate-mapping mice to trace PD-1-expressing cells via tdTomato during PD-1 blockade. PD-1-fate-mapped lymphocytes downregulated PD-1 in the spleen but largely retained it in tumors, except for NK cells, which lost PD-1 and regained function. Single-cell transcriptional profiling was performed on immune cells in PD-L1-low Lewis lung carcinoma (LLC) treated with cyclophosphamide (CTX) and/or anti-PD-1 antibodies. Anti-PD-1 monotherapy showed limited efficacy, whereas CTX plus anti-PD-1 markedly improved tumor control. Single-cell analysis identified 15 transcriptionally distinct immune clusters with treatment-dependent abundances. Combination therapy expanded cytotoxic CD8 T cells and a dysfunctional Treg cluster, enhancing CTL activity, including PD-1-fate-mapped CD8 T cells expressing Tpex1 markers. Single-cell TCR analysis revealed that clonotypes selectively expanded by combination therapy, mediating potent cytotoxicity against LLC tumors. PD-1 blockade synergizes with cytotoxic chemotherapy to diversify and expand PD-1 lineage-traced CTL clonotypes, driving robust antitumor immunity. Thus, our fate-mapping system is a valuable tool to search for immune cells responsive to ICI therapy.