Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells

We used single-cell mRNA sequencing to analyze the response of tumor-specific CD4+ tumor infiltrating lymphocytes (TILs) and draining lymph node (dLN) T cells. Computational approaches to characterize subpopulations identified TIL transcriptomic patterns strikingly distinct from acute and chronic anti-viral responses and dominated by diversity among T-bet-expressing T helper type 1 (Th1)-like cells. In contrast, the dLN response includes T follicular helper (Tfh) cells but lacks Th1 cells. We identify a type I interferon-driven signature in Th1-like TILs and show that it is found in human cancers, in which it is negatively associated with response to checkpoint therapy. Overall design: Single-cell RNA sequencing of CD4+ T cells specific for a defined recombinant tumor antigen, sorted from the tumor microenvironment and draining lymph nodes.