Fig. 4

Evolution of the tumor microenvironment on treatment. A CD4, CD8, and PD-L1 density in baseline and post-treatment biopsies. Circles indicate clinical responders and squares non-responders. The difference between baseline and post-treatment was not significant (Mann–Whitney test, CD4 p = 0.69; CD8 p = 0.69; PD-L1 p = 0.84). B Linear regression analysis of difference in CD8 density between post-treatment and baseline versus maximum T cell proliferation response (Pearson’s correlation, p = 0.22). C Copy number status of HLA/TAP and hTERT genes post-treatment. D HLA class I and II expression in baseline and post-treatment biopsies. The p values represent unpaired t test for difference between baseline and post-treatment expression levels. E IFN-γ signature in baseline vs. post-treatment biopsies. F Overlapping single nucleotide variants and G predicted neoantigens between baseline and post-treatment biopsies. IR immune response, TIL tumor-infiltrating lymphocytes, R clinical responder, NR clinical non-responder, BL baseline, PT post-treatment, NS not significant, TPM transcripts per million, ND not detected