Joy A. Pai, Matthew D. Hellmann, Jennifer L. Sauter, Marissa Mattar, Hira Rizvi, Hyung Jun Woo, Nisargbhai Shah, Evelyn M. Nguyen, Fathema Z. Uddin, Alvaro Quintanal-Villalonga, Joseph M. Chan, Parvathy Manoj, Viola Allaj, Marina K. Baine, Umesh K. Bhanot, Mala Jain, Irina Linkov, Fanli Meng, David Brown, Jamie E. Chaft, Ansuman T. Satpathy
Cancer Cell, 30 March 2023

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