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. 2020 Aug 6;5(15):e138290. doi: 10.1172/jci.insight.138290

Figure 2. Successful LCM yields compartment-specific protein identification and biology enrichment.

Figure 2

(A) Unsupervised hierarchical clustering of known tumor and stromal protein markers shows mutually exclusive expression patterns. (B) ssGSEA of previously published and newly created mouse/human PDX tumor and stroma gene sets (17) was performed, showing enrichment in concordance with compartment specificity. Data are shown in heatmap. Each column represents a tumor (n = 15) or stroma sample (n = 16). Each row represents a gene set that was used for enrichment. Colors indicate the enrichment score. (C) Radar plots of GSEA performed on “Hallmarks of cancer” and “KEGG pathways” (D) between sample origin reveal divergent biology of PDAC tumor and stroma, where bulk samples resemble stromal biology. Significant enriched gene sets were identified with GAGE (56), and the top 5 gene sets from each tissue origin with a P value of less than 0.05 are visualized.