Fig. 2

A molecular signature of de novo metastasis progression. a Principal component analysis (PCA) comparing expression profiles from pre-metastatic (pre-met, blue) or post-metastatic (post-met, red) primary tumors, or lung metastases (lung, black) from NPK mice (n = 8/group). Note that Principal Component 1, capturing 40.6% of gene expression variance, effectively distinguishes pre-metastatic tumors from post-metastatic tumors and lung metastases. b GSEA comparing a reference signature of mouse lung metastases (lung mets) versus pre-metastatic tumors to a query signature of mouse post-metastatic versus pre-metastatic tumors. c, d Heat map representations of differentially expressed genes from the positive and negative leading edges, respectively, from the GSEA in panel b. The color key shows relative expression levels of the differentially expressed genes (red corresponds to overexpressed genes while blue corresponds to underexpressed genes). e Pathway enrichment analysis using the mouse metastasis progression signature defined between lung metastasis versus pre-metastatic tumors, as in panel b, to query the hallmark pathways dataset from the molecular signatures database (MSigDB). Red and blue nodes indicate positive and negative enrichment, respectively (p < 0.05). Thickness of arrows indicate the overlap of genes in the leading edges. The p-values correspond to the GSEA enrichment, and the relative size of the node indicates the relative p-value, as shown. f Cross-species GSEA comparing a reference mouse metastasis progression signature (lung metastasis versus pre-metastatic tumors, as in panel b) with a query gene set from a human metastasis signature defined between bone metastasis biopsies versus primary tumors from Balk et al. (Supplementary Table 1). For GSEA, red vertical bars indicate overexpressed query genes and blue vertical bars indicate underexpressed query genes. GSEA were done using the top 200 differentially expressed genes; p-values were calculated using 1000 gene permutations. ES: enrichment score, NES: normalized enrichment score