Extended Data Fig. 3: Cellular determinants of response and resistance to anti-PD-1.

a, Changes in tumor PD-L1 pre- versus post-treatment using immunohistochemistry staining (n = 9 independent paired patient samples). **P <0.01 using two-sided Wilcoxon matched-pairs test. b, Correlation of percentage of Ki67⁺ in non-naïve CD8 T cells versus percentage of Ki67⁺ in Tregs (FoxP3⁺CD4) (n = 21 independent patient samples); R score and P value generated using Pearson’s correlation. c, Thirty-three post-treatment immune parameters classified by recurrence using random forest analysis and ranked by importance score (n = 21 independent patient samples). Error bar denotes mean ± s.d. for 1,000 random forest iterations. d, Percentage expression of selected markers in tumor between patients with recurrence (9 independent patient samples) and no recurrence (12 independent patient samples). P value calculated using two-sided Mann–Whitney test. e, Correlation of percentage of Ki67⁺ in Tregs (FoxP3⁺ CD4) versus percentage of Eomes⁺ T-bet^- in non-naïve CD8 (n = 21 independent patient samples); R score and P value generated using Pearson’s correlation. f, Twenty-five pretreatment immune parameters classified by recurrence using random forest analysis and ranked by importance score (n = 21 independent patient samples). Error bar denotes mean ± s.d. for 1,000 random forest iterations. g, Percentage expression of selected markers in tumor between patients with recurrence (9 independent patient samples) and no recurrence (12 independent patient samples). Two-sided t-test was used for CD45RA^-CD27⁺ and CD45RA⁺CD27⁺ comparisons. Two-sided Mann–Whitney test was used for CD8 Ki67⁺ and CD4 Ki67⁺ comparisons. Error bar denotes mean ± s.d. h, Scatter plot of percentage of Ki67⁺ in non-naïve CD8 versus percentage of Ki67⁺in FoxP3⁺ CD4 (Tregs) at pretreatment stratified by recurrence status. Dotted line denotes non-naïve CD8 Ki67⁺ of 5.5 calculated by CART analysis as the optimal cut point separating recurrence versus no recurrence (n = 21 independent patient samples).