Extended Data Fig. 3: Differences in absolute abundance of immune cell subsets derived from RNAseq deconvolution from baseline to on-therapy in the SBRT and control groups.
(a–v) A significantly greater abundance of CD8 T cells (mean SBRT baseline 0.244, mean SBRT on-therapy 0.765, Mann Whitney-U test (two-sided) P = 0.027) and M1 macrophages (mean SBRT baseline 0.099, mean SBRT on-therapy 0.292, Mann Whitney-U test (two-sided) P = 0.013) were noted on-therapy in the SBRT arm. We also observed a trend towards a higher abundance of activated CD4 memory T cells (mean SBRT baseline 0.008, mean SBRT on-therapy 0.083, Mann Whitney-U test (two-sided) P = 0.074) and activated NK cells (mean SBRT baseline 0.134, mean SBRT on-therapy 0.361, Mann Whitney-U test (two-sided) P = 0.090) on-therapy compared to baseline in the SBRT arm. These differences were less pronounced in the control arm (CD8 T cells mean control baseline 0.320, mean control on-therapy 0.525, Mann Whitney-U test (two-sided) P = 0.248; activated CD4 memory T cells mean control baseline 0.010, mean control on-therapy 0.087, Mann Whitney-U test (two-sided) P = 0.732; activated NK cells mean control baseline 0.156, mean control on-therapy 0.259, Mann Whitney-U test (two-sided) P = 0.222; M1 macrophages mean control baseline 0.135, mean control on-therapy 0.275, Mann Whitney-U test (two-sided) P = 0.121). A trend towards a higher abundance of M2 macrophages in on-therapy compared to baseline samples was noted in the control group, while such a difference was not noted in the SBRT group (mean control baseline 0.506, mean control on-therapy 0.883, Mann Whitney-U test (two-sided) P = 0.069; mean SBRT baseline 0.562, mean SBRT on-therapy 0.943, Mann Whitney-U test (two-sided) P = 0.274). Absolute abundance values and statistics related to all other cell types determined by RNA-seq deconvolution are listed in Supplementary Table 12. Sample sizes for all panels are: SBRT Baseline n = 14 samples, SBRT on-therapy n = 12 samples, control baseline n = 12 samples, control on-therapy n = 10 samples. Box plots depict the median value and hinges correspond to the first and third quartiles. The whiskers extend from the corresponding hinge to the furthest value within 1.5* the interquartile range from the hinge.
