Fig. 2

Baseline tumor microenvironment. A Clinical outcome and genomic characteristics of patients with available biopsies at baseline. Genes in red font are related to immunotherapy resistance [45], and genes in blue telomerase expression. Green squares indicate non-synonymous mutations. B Gene copy alterations of TERT, HLA, and TAP. C Fraction of Sox10/S100 cells also positive for hTERT based on immunofluorescence staining (dotted line represents the median, 72.7%). D Representative immunofluorescence staining of tumor biopsies. CD4 is stained cyan, CD8 is stained blue, hTERT is stained red, and Sox10/S100 is stained green. Image 1 is from patient N04 at baseline, and image 2 from patient N06 at baseline. The hTERT dense area in the top right of image 2 is likely a hair follicle. E Linear regression analysis of immune response (maximum stimulation index (SI)) and hTERT + Sox10/S100 + cell density based on immunofluorescence staining. The association is not significant (Pearson’s correlation, p = 0.47). F Baseline CD4, CD8, and PD-L1 density in responders (R) and non-responders (NR) (Mann–Whitney test, CD4 p = 1.0; CD8 p = 0.71; PD-L1 p = 0.90). Baseline hTERT intensity in melanoma cells was significantly lower in clinical responders (Mann–Whitney test, p = 0.04). G Hierarchical clustering of baseline IFN-γ signature using the Euclidean distance. The grey box indicates missing data (HLA-DQA1 only). H Baseline PBMC and tumor TCR repertoire diversity and I clonality according to RECIST 1.1 response categories. BOR, best overall response; ns, not significant; ND, not detected. *Patient N04 only had week 12 biopsy available for whole-exome and RNA sequencing. The BRAF status was based on a diagnostic biopsy for this patient