Functional state of lung cancer-reactive cytotoxic T cells is shaped during 2 T cell priming and determines sensitivity to immunotherapy

In non-small cell lung cancer (NSCLC), response to checkpoint blockade therapy (CBT) is associated with PD-L1 expression, induced by IFN-g-producing, tumor-infiltrating CD8+ T cells. However, not all tumors with a CD8+ T cell infiltrate respond to CBT, and little is known about the mechanisms governing CBT resistance in T cell-infiltrated NSCLC. We used a pre-clinical orthotopic NSCLC mouse model to study CBT-refractory CD8+ T cell responses. Single-cell RNA sequencing revealed that lung cancer-specific tumor-infiltrating CD8+ T cells exhibited clonal expansion but lacked expression of genes associated with effector and exhausted T cell responses, indicating that they underwent a differentiation program distinct from conventional T cell exhaustion. Mechanistic studies revealed that this lung cancer-specific T cell dysfunction program was established early during priming in the mediastinal lymph node. This program was characterized by robust T cell proliferation and acquisition of lung-homing factors but a failed upregulation of markers of effector and exhausted T cells. Intriguingly, CD8+ T cells from NSCLC patients expressed an analogous gene expression program which was associated with lung cancer specific T cell dysfunction and distinct from conventional T cell exhaustion. As a proof-of-concept that this lung cancer-specific T cell differentiation program could be therapeutically manipulated, we administrated recombinant IL-2 and IL-12, which was sufficient to restore effector T cell differentiation and induce control of lung tumors. These findings imply that a lung cancer-specific CD8+ T cell differentiation trajectory, activated during T cell priming in the mediastinal lymph node, limits the response of CD8+ T cells to CBT and thereby contributes to failed responses following CBT in T cell-infiltrated NSCLC. Overall design: Analysis of tumor-infiltrating cells from mice bearing either flank or lung KP tumors. Single-cell of SIY-specific cells: FlankSIY (treatment: Flank) LungSIY (treatment: Lung) BulkRNA of 2C cells: 2C_Flank* (treatment: Flank), 2C_Lung* (treatment: Lung)