Fig. 3: Expression of Ecad and NGFR defines molecular subgroups of MBM.

a Separation of MBM regarding the presence of Ecad- or NGFR-associated genes as identified in this study. Intermediate-state tumors (Pt.1, Pat8/M4, 22) feature expression of both signatures, at least partly. Molecular subgroups (BRAF^mut vs. wt) and Ecad/NGFR states are color coded. Heat map presents a supervised, euclidean, ward.D clustering. PLXNC1 (Plexin C1), ABCB5 (ATP Binding Cassette Subfamily B Member 5) and MITF (Melanocyte Inducing Transcription Factor) or LOXL2/LOXL3 (Lysyl Oxidase Like 2/3) among others served as markers of Ecad^high or NGFR^high states, respectively. b IHC of selected MBM for Ecad, NGFR and CD3 validated proper expression of investigated markers and assigned molecular subtypes. Hematoxylin&Eosin (H&E) staining depicts morphological differences of tumors cells. c GSEA of Ecad^high and NGFR^high subsets showing enrichment of proliferative and invasive phenotypes. FDR indicates the significance of enrichment, ES enrichment score, NES normalized enrichment score. 10,000 permutations were performed. d Box plots depicting the levels of CD3D and CD8A of MBM defined as TIL^high and TIL^low, ranked by expression levels of CD3D, n = 16 biologically independent tumors were investigated. e Left panel: GSEA of TIL^high and TIL^low MBM demonstrating a high inflammatory response in TIL^high MBM. Right panel: Characterization of TIL^high and TIL^low MBM by CIBERSORT and ESTIMATE clearly discriminate tumors regarding levels of T cells (CD4, CD8), macrophages, monocytes and mast cells. Significance was determined by a unpaired two-tailed, t-test. Box and whisker plots show median (center line), the upper and lower quartiles (the box), and the range of the data (the whiskers), including outliers (d). Source data are provided as a Source Data file.