Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade

Paired single-cell RNA and T cell receptor sequencing (scRNA/TCR-seq) has allowed for enhanced res-olution of clonal T cell dynamics in cancer. Here, we report a scRNA/TCR-seq analysis of 187,650 T cells from 31 tissue regions, including tumor, adjacent normal tissues, and lymph nodes (LN), from three patients with non-small cell lung cancer after immune checkpoint blockade (ICB). Regions with viable cancer cells are enriched for exhausted CD8+ T cells, regulatory CD4+ T cells (Treg), and follicular helper CD4+ T cells (TFH). Tracking T cell clonotypes across tissues, combined with neoanti-gen specificity assays, reveals that TFH and tumor-specific exhausted CD8+ T cells are clonally linked to TCF7+ SELL+ progenitors in tumor draining LNs, and progressive exhaustion trajectories of CD8+ T, Treg, and TFH cells with proximity to the tumor microenvironment. Finally, longitudinal tracking of tu-mor-specific CD8+ and CD4+ T cell clones reveals persistence in the peripheral blood for years after ICB therapy.

Automated summary

Paired single-cell RNA and T cell receptor sequencing (scRNA/TCR-seq) provides insight into clonal T cell dynamics in non-small cell lung cancer patients after immune checkpoint blockade therapy. The analysis revealed enrichment of exhausted CD8+ T cells, regulatory CD4+ T cells (Treg), and follicular helper CD4+ T cells (TFH) in regions with viable cancer cells. Additionally, the study demonstrated clonal linkage between TFH and tumor-specific exhausted CD8+ T cells and TCF7+ SELL+ progenitors in tumor draining lymph nodes, as well as progressive exhaustion trajectories of CD8+ T, Treg, and TFH cells in proximity to the tumor microenvironment. Longitudinal tracking also showed persistence of tumor-specific CD8+ and CD4+ T cell clones in the peripheral blood for years after immune checkpoint blockade therapy.