Fig. 6: Clinical benefit in individual patients with high T-cell infiltration.

A Deconvolution results for 14 samples of patients treated with immune checkpoint inhibitors from the MASTER cohort, also including additionally integrated data from a validation cohort of 4 patients (red font). Barplot shows proportions of major immune cell subpopulations. Samples were ordered by T-cell to macrophage ratio and annotated by tumor entity and therapy status (ICI prior to sequencing). Top bars indicate the absolute immune score and TMB. The red lines depict median scores. Patients achieving a clinical benefit were marked in red. B Deconvolution results for 14 samples from the Vos et al pre-treatment cohort. For details see panel A. TMB results were missing for this cohort. C Additional validation in a separate cohort of 5 patients treated with ICI using immunohistochemistry. Staining intensities of CD68 and CD3 were normalized to sum up to 1. Samples were annotated by tumor entity and sorted by T-cell proportions. Clinical benefit was observed in the patient with the highest T-cell/macrophage ratio (highlighted in red). D Immunohistochemical CD3 staining revealed the presence of T-cells in the patient achieving a clinical benefit from C. E Immunohistochemical CD68 staining depicting some presence of macrophages in the same patient. Deconvoluted, p-value filtered T-cell proportions (F) and T-cell to macrophage ratios (G) in samples that received ICI prior to sequencing (n = 6, median T-cell proportion = 0.28, iqr = 0.12, max = 0.43, min = 0.16; T-cell/macrophage ratio = 0.81, iqr = 0.61, max = 2.04, min = 0.39) or did not receive ICI before sequencing (n = 54, median T-cell proportion = 0.25, iqr = 0.17, max = 0.41, min = 0.03; T-cell/macrophage ratio = 0.65, iqr = 0.62, max = 1.96, min = 0.04) revealed no significant changes in tumor immune microenvironment composition after ICI treatment, although a modest increase in T-cell levels was observed (Wilcoxon test, two-sided).