Fig. 2: Responders had an increase in effector T cells within the TME.
a, viSNE plot of CD45+ cells in the TME of patients pre- and post-treatment stratified by response and colored by cell type. Density plots of two clusters are included below the viSNE plot (nonresponders n = 6 patients, responders n = 10 patients). b, Histograms representing the proportion of cells, within the cytokine-producing T cell cluster, producing IFN-γ and expressing TCF1. c, Histograms representing the proportion of cells, within the CD103+CD39+ CD8 T cell cluster, expressing Ki-67 and TCF1. d, t-Distributed stochastic neighbor embedding (t-SNE) plots of CD45+ cells in a responder and two nonresponders. Blue represents TME samples taken before treatment, and pink represents TME samples taken after treatment. e, Magnification of the large cluster of pathways increased in responders pre-treatment represented in Extended Data Fig. 3b (nonresponders n = 5 patients, responders n = 8 patients). f, Significant genes determined using the GSEAPreranked module, based on an adjusted P value to account for multiple comparisons, which were used in the gene mapping identified pre-treatment (nonresponders n = 5 patients, responders n = 8 patients). The gray bars denote pathological response. g, Average of the top 5 TCR sequences (nonresponders n = 3 patients, responders n = 5 patients). h, Scatterplot with annotations depicting clones with more than 8 transcripts before and after treatment for patients 01-010 and 01-014. Red dots were clones significantly increased pre-treatment and blue dots were clones that were significantly increased post-treatment. i, Quantification of CD8+ T cells (CD3+CD8+) within the TME pre- and post-treatment (nonresponders n = 5 patients, responders n = 7 patients). j, Quantification of VECTRA images of CD4 T cells (CD3+CD8−Foxp3−) within the TME pre- and post-treatment (nonresponders n = 5 patients, responders n = 7 patients). k, CPS (no. PD-L1-expressing cells/no. CK+ cells) calculated from VECTRA images (nonresponders n = 6 patients, responders n = 12 patients). l, Quantification of VECTRA images of PD-1-expressing T cells (CD3+PD-1+) within the TME pre- and post-treatment (nonresponders n = 6 patients, responders n = 12 patients). m, The percentage of cells expressing PD-L1 from VECTRA images (mean ± s.e.m.) (nonresponders n = 6 patients, responders n = 12 patients). n, Quantification of the median proximity of a CD8+ cell to a CK+ cell from VECTRA images (nonresponders n = 6 patients, responders n = 12 patients). o, Representative images of the distance between cancer cells (CK+) and the nearest CD8 T cells (highlighted in red). Statistical significance was determined using a two-tailed paired Student’s t-test. *P < 0.05, **P < 0.01, ***P < 0.001. NR, non-responder; R, responder.
