Fig. 4. Comparisons between responders and nonresponders of pretreatment TCF1 and SIGLEC-7 gene expression, neutrophil and mast cell signatures, TMB, infiltration of immune cell subsets and driver gene mutations.

a–d, Pretreatment gene expression in nonresponders (NR, n = 5) versus responders (R, n = 14) of TCF1 (a), neutrophil signature (b), mast cell signature (c) and SIGLEC-7 (d). Boxplots represent the median, 25th and 75th percentiles; whiskers extend from the hinge to the largest value below 1.5 * IQR from the hinge. The difference between NR and R was tested using a two-sided Wilcoxon Rank-sum test. e, TMB (number of nonsynonymous mutations per megabase of protein coding genome, y axis, log₁₀scale) in nonresponders (NR, n = 5) versus responders (R, n = 14). Blue stars indicate patients with dMMR tumors. Box plots represent the median, 25th and 75th percentiles; whiskers extend from the hinge to the largest value below 1.5 × IQR from the hinge. The difference between NR and R was tested using a two-sided Wilcoxon rank-sum test. f, Heatmap of baseline RNA expression (Z-scores) of TME-specific signatures for leukocytes (CD45), cytotoxic cells, T cells, CD8 T cells, exhausted CD8 T cells, CD4 T cells, T_reg cells, B cells, NK cells, eosinophils, macrophages, mast cells and neutrophils. Patients (x axis) were ordered on the basis of hierarchical clustering (upper dendrogram). The squares below indicate Lauren classification, EBV status, MMR status, TMB (log₁₀scale) and pathologic response per patient. The association of signature expression with response is shown on the right as a lollipop plot of signed, two-sided Wilcoxon rank-sum test-based P values (unadjusted for multiple hypothesis testing; x axis on log₁₀ scale). g, Mutational status of all cancer-driver genes altered in ≥3 patients (colors denote the mutation type), alteration frequency (bar plot) and association with response (lollipop plot of signed, two-sided Fisher’s exact test-based P values (unadjusted for multiple hypothesis testing; xaxis on log₁₀ scale). The squares below indicate Lauren classification, EBV status, MMR status, TMB (log₁₀ scale) and responder status per patient. n.s., not significant.