Single-cell clonal lineage tracing identifies the transcriptional program controlling the cell-fate decisions by neoantigen-specific CD8+ T cells.

Abstract

Neoantigen-specific T cells recognize tumor cells and are critical for cancer immunotherapies to be effective. However, the transcriptional program controlling the cell-fate decisions by neoantigen-specific T cells is incompletely understood. Here, using joint single-cell transcriptome and T-cell receptor (TCR) profiling, we mapped the clonal expansion and differentiation of neoantigen-specific CD8+ T cells in the tumor and draining lymph node in mouse prostate cancer. Neoantigen-specific CD8+ tumor-infiltrating lymphocytes (TILs) upregulated gene signatures of T-cell activation and exhaustion compared to those recognizing other tumor antigens. In the tumor-draining lymph node, we identified TCF1+TOX- TSCM, TCF1+TOX+ TPEX, and TCF1-TOX+ effector-like TEX subsets among neoantigen-specific CD8+ T cells. Divergent neoantigen-specific CD8+ T-cell clones with balanced distribution across multiple differentiation fates underwent significantly greater expansion compared to clones biased towards TEX, TPEX, or TSCM. The TPEX subset had greatest clonal diversity and likely represented the root of neoantigen-specific CD8+ T-cell differentiation, whereas highly clonally expanded effector-like TEX cells were positioned at the branch point where neoantigen-specific clones exited the lymph node and differentiated into TEX TILs. TSCM differentiation of neoantigen-specific CD8+ T-cell clones in the lymph node negatively correlated with exhaustion and clonal expansion of the same clones in the tumor. In addition, the gene signature of neoantigen-specific clones biased toward tumor infiltration relative to lymph-node residence predicted a poorer response to immune checkpoint inhibitors by cancer patients. In conclusion, we have identified a transcriptional program that controls the cell-fate choices by neoantigen-specific CD8+ T cells and correlates with clinical outcomes in cancer patients.