Fig. 5: CD3⁺CD8⁺ T cell infiltration impacts the HLA-II immunopeptidome.

a–c, Contribution of immune cells to the HLA-II immunopeptidome based on sampling scores of immune cell markers in tumors annotated as excluded (n = 29 tumor macro-regions) (a) and infiltrated (n = 15 tumor macro-regions), nonsmokers (n = 21 tumor macro-regions) and smokers (n = 23 tumor macro-regions) (b) and immune-high (n = 27 tumor macro-regions) and immune-low (n = 17 tumor macro-regions) (c) per cell type. P values were calculated using one-sided Wilcoxon’s test. The boxplots show the median (line), the IQR between the 25th and 75th percentiles (box) and 1.5× the IQR ± the upper and lower quartiles, respectively. No adjustments were made for multiple testing. d, The z-score distribution of the gene expression comparisons of tumor versus stroma + TLS + CD45⁺ micro-regions in the infiltrated-high samples. Genes in the upper quartile are more highly expressed in tumor micro-regions whereas those in the lower quartile are highly expressed in stroma micro-regions. e, Example of correlation of CD79B expression and B cell abundance in infiltrated-high samples (n = 26 stroma + TLS + CD45⁺ and tumor micro-regions). The error bands represent the 95% CI. f, The z-score distribution of the gene expression comparisons of tumor versus stroma + TLS + CD45⁺ micro-regions in excluded-high samples. g, Example of correlation of CD14 expression and macrophage abundance in excluded-high tumors (n = 34 stroma + TLS + CD45⁺ and tumor micro-regions). The error bands represent the 95% CI. h,i, Correlation of all genes attributed to stroma + TLS + CD45⁺ micro-regions (lower quartile) or with tumor micro-regions (upper quartile) with cell-type abundance in infiltrated-high (h) and excluded-high (i) samples. DCs, dendritic cells; NK cells, natural killer cells; T_reg cells, regulatory T cells. j,k, Sum of sampling score for genes correlates with different immune cell type (Pearson’s correlation r > 0.5) in infiltrated-high (n = 2 patients and n = 163 genes) (j) and excluded-high (n = 3 patients and n = 168 genes) (k).