Figure 2

Concordant DNA methylation and gene profiles between HNSC and LUSC subtypes: (a) Heatmap of a correlation matrix illustrating pair-wise Pearson correlations of DNA methylation profiles between 528 HNSC patients (columns) and 503 LUSC patients (rows). Correlation coefficients indicate the correlation of each patient pair across 621 CpG sites, representing all CpG sites that were available for all patients (Measured on both Illumina 27 k and 450 k arrays), and which were abnormally methylated (hypermethylated in hypomethylated) in all or a subset of HNSCs. Patients are ordered according to DNA methylation subtypes (no clustering was performed), with sidebars indicate HNSC and LUSC subtypes (NSD1 subtypes illustrated in red, other subtypes grey). NSD1 mutation and deletion sidebars indicate patients with NSD1 mutations or deletions (black), absence of NSD1 mutations or deletions (grey), or missing data (white). The ‘NSD1 PAM class’ sidebar indicates predictions of PAM models for belonging to the NSD1 subtype, which were trained on one cancer type and used to classify patients of the other cancer type as either ‘NSD1 subtype’, or ‘Other subtype’ (e.g., ‘HNSC PAM class’ refers to predictions made by a model trained on HNSC subtypes and applied to predict subtypes of LUSC patients). (b) Scaled mean RNA expression in LUSC DNA methylation subtypes of genes that were upregulated (HNSC up) and downregulated (HNSC down) in the HNSC NSD1 subtype. Asterisks indicate the significance of differential mean expression between the NSD1 LUSC subtype (Red box) and each other subtype (Wilcoxon rank sum test): NS Not significant, *P < 0.05, **P < 0.01, ***P < 0.001. (c) DNA methylation of development-related transcription factor genes, in normal tumor-adjacent tissue (purple), and in tumor of patients within NSD1 subtypes (red) or other subtypes (grey), in HNSC and LUSC.