Fig. 4

Immune cell infiltration in PeM. a Correlation between immune score and stromal score derived for each tumor sample using mRNA expression and protein expression. b Estimated relative mRNA fractions of leukocytes infiltrated in PeM tumors based on CIBERSORT analysis. c CD3 and CD8 immunohistochemistry showing immune cell infiltration on BAP1^del PeM (photomicrographs magnification, × 20). d mRNA expression differences in immune checkpoint receptors—LAG3, PD1, CTLA4, CD28, ICOS, BTLA, and HAVCR2 between PeM subtypes. Other genes in the figures are interacting receptors of the immune checkpoint markers mentioned above. The bar plot of the top of the heatmap indicates BAP1 mRNA expression levels. The colors on the bar indicate BAP1 copy number status. The bar plot on the right represents the negative log10 of Wilcoxon signed-rank test p value of individual immune checkpoint receptors computed between PeM subtypes. The expression levels are log2 transformed and mean normalized