Figure 6a, iCAF T-cell dysfunction gene signature highlighting genes significantly associated with CTL dysfunction in two out of three independent patient cohorts (METABRIC, GSE21653 and GSE58812). b, Representative cohort (METABRIC) showing the prognostic value of iCAF T-cell dysfunction signature in the context of CTLs for a total of 233 patients. Kaplan-Meier's present two groups of patients, 'low CTL' (blue line) and 'high CTL' (red line), as estimated according to the average expression of CTL-specific genes and stratified as compared to the mean. Tumours with low iCAF T-cell dysfunction signatures (top) show patients with high CTL levels have a better survival outcome. In contrast, this survival benefit is lost in tumours with a high iCAF T-cell dysfunction signature (bottom). P-values were defined from the Cox proportional hazard (Cox-PH) model. c, Dysfunctional CTLs detected in all five TNBC patients determined through scoring a T-cell exhaustion signature. UMAP featureplot of the exhaustion signature across all stromal and immune cells as in Fig. 1D. d, Bulk stromal signature associates with CTL exclusion. Pearson correlation was computed between all inferred CTL levels (y axis) and the respective correlation between the bulk sample and the single-cell cluster (x axis). Signature of all stromal cells divided over all cells correlated negatively with CTL levels, while control CD4+ and CD8+ gene signatures show a positive correlation. P-values were computed using a two sided t-test for correlation, and were adjusted using the Benjamini-Hochberg procedure. e, dPVL cells associated with CTL exclusion. Repeated analysis in the same manner as in (d), instead with myCAF, iCAF, dPVL and imPVL clusters divided over all stromal cells independently, highlighting that CTL exclusion is mainly driven by dPVL cells. Representative cohort GSE58812 is shown. , dPVL profiles and CTL exclusion consistent in our study. f, Patients with the highest dPVL profiles by scRNA-Seq (P4 and P5) show the lowest Tumour infiltrating lymphocyte (TIL) pathology counts. n = 5 stromal 1 mm2 regions were counted per tumour. The central band, boxes and whiskers represent the median, lower/upper quartile and min/max CTL counts per 1mm2, respectively. P3 is shown as an example of a low dPVL profile with high CTLs. In contrast, P4 has a high dPVL profile with low CTLs. Statistical significance was determined using pairwise comparison with Student's t test with p‐values denoted by asterisks: *p < 0.05, **p < 0.01, ***p < 0.001 and ****p < 0.0001. dPVL profiles and CTL exclusion consistent in our study. g-h, Accurate quantification of CTLs (g) and representative immunohistochemistry staining for CD8 on matched patient tumour sections (h). n = 5 stromal 1 mm2 regions were counted per tumour. The central band, boxes and whiskers represent the median, lower/upper quartile and min/max CTL counts per 1mm2, respectively. P3 is shown as an example of a low dPVL profile with high CTLs. In contrast, P4 has a high dPVL profile with low CTLs. Statistical significance was determined using pairwise comparison with Student's t test with p‐values denoted by asterisks: *p < 0.05, **p < 0.01, ***p < 0.001 and ****p < 0.0001.