Fig. 3: Tumor cells states in immune checkpoint blockade (ICB) resistant melanoma.

A Heatmap displaying expression of five melanoma state specific genes (MITF, TAP1, MKI67, NGFR, AXL) across 2,766 tumor cell enriched spots from the Visium data in six melanoma tumors. Spots were divided in five distinct clusters based on consensus clustering and are grouped by this cluster assignment. B Mapping back melanoma cell clusters as defined in A, from six melanoma metastases, to the respective histological images. Indicated is also a validation using multiplex immunofluorescence. C MITF multiplex immunofluorescence intensity of n = 51 ICB naïve, n = 10 anti-CTLA4 resistant (CTLA4res), n = 8 anti-PD1 resistant (PD1res) and n = 6 anti-PD1 resistant under BRAFi treatment (PD1res*). MITF intensity was measured in SOX10 positive melanoma cells. P-value from Wilcoxon test. Test was two-sided. * denotes a melanoma with an MITF-high phenotype and B2M deep deletion. Scalebars are indicated by white line and correspond to 100 μm. Boxplot is displayed with the center-line as median, the box limits as lower and upper quartiles, and with whiskers covering the most extreme values within 1.5 x Interquartile-Range. D Frequency plot of different melanoma cell states using multiplex immunofluorescence of MITF/B2M fractions and NGFR fractions. NGFR fractions are within SOX10 positive melanoma cells. Samples are sorted by CD8 fraction and grouped according to treatment. (PD1res n = 8, PD1res* n = 7, CTLA4res n = 10, ICB naïve n = 53). Source data are provided as a Source Data file.