Fig. 2: Precursor exhausted cells drive clone expansion and are preferentially maintained in the tumor during clone contraction.

a Cells from tumors excised on days 14 and 21 (n = 7 mice) were sorted based on marker expression before processing through bulk TCR-sequencing, enabling phenotypic characterization of individual clones. Clones containing TIM-3⁺ cells were selected for downstream analysis as in Supplementary Fig. 2a. b Velocity plot depicting the cellular composition changes of expanding and contracting clones from day 14 to 21. Arrows depict individual clones. The base of the arrow indicates the fraction of cells that were precursor exhausted and terminally exhausted on day 14 while the arrow direction and length indicate the magnitude and vector of change in these fractions over time. c, d Change in the number of precursor and terminally exhausted cells between day 14 and 21 colored by their expansion dynamics (c) and fraction of cells terminally exhausted on day 14 (d). Symmetrical log axis with a linear range of -20 to +20 (as depicted by gray lines on axes). e Expansion and contraction phases of clones. Expanding and contracting clones from the 7 mice that displayed changes in both the precursor exhausted and terminally exhausted cell fractions are shown (b−d). Dots represent clones (c, d). Illustrations created with cartoons from BioRender (Ueha, S. (2025) https://BioRender.com/yx373li) and Irasutoya.com (a). Source data are provided as a Source Data file.