Fig. 4: Immune microenvironment.

a Immune microenvironment deconvolution of immune cell fractions stratified by time point and response (n = 6 R and n = 8 NR). b IHC validation (x axis) of the deconvolution of CD8⁺ T-cell proportion estimated from RNASeq (y axis) (Spearman correlation coefficients rho (r) and associated p values from two-tailed correlation test are provided for R and NR groups, samples from n = 15 R and n = 16 NR). c Density of CD8 T cells by location from IHC in the tumor core (samples from n = 15 R and n = 16 NR), and peritumoral (samples from n = 9 R and n = 13 NR) (p value from two-sided Student’s t test between R and NR groups). d Scatterplot between the T-cell receptor clonality (B locus) and CD8⁺ T-cell (left) and NK cell abundances (right) (Pearson’s correlation coefficient (r)) and associated p values from two-tailed correlation test are provided for R (n = 6) and NR (n = 8) groups). a, c Box plots show the median as center, the lower and upper hinges that correspond to the 25th and the 75th percentile, and whiskers that extend to the smallest and largest value no >1.5*IQR. Values that stray more than 1.5*IQR upwards or downwards from the whiskers are considered potential outliers and represented with dots. b, d Bands represent confidence intervals (±0.95) around a linear model fitted by robust regression using an M estimator. Source data are provided as a Source Data file.