Fig. 2.
The Inflamed subtype is immune rich. a Pathway enrichment of significantly different proteins (±1.5 fold-change and Wilcoxon Padj ≤ 0.05 compared to the rest of the cohort). The Inflamed subtype was enriched for immune pathways including neutrophil degranulation. b–d Immune, Stromal, and ESTIMATE scores from the ESTIMATE algorithm18. The Inflamed subtype had the highest median Immune score. e–o Box plots showing CIBERSORT results for each immune subtype compared across the three proteomic subtypes and between Inflamed A and Inflamed B7. Inflamed had significantly higher proportions of memory B-cells (Wilcoxon P = 5.73E-03), monocytes (Wilcoxon P = 3.78E-04), and neutrophils (Wilcoxon P = 0.021) compared to the other subtypes, and plasma cells were significantly lower (Wilcoxon P = 0.048). M2 macrophages were significantly higher in Redox (Wilcoxon P = 0.016), and resting NK cells were higher in Mixed (Wilcoxon P = 0.027). Regulatory T-cells were significantly higher in Inflamed B (Wilcoxon P = 0.039), and neutrophils were significantly higher in Inflamed A (Wilcoxon P = 0.025). box plots Significance was denoted using the following: * = P < 0.05, ** = P < 0.01, *** = P < 0.001. The center line indicates the median, the bounds of the box indicate the interquartile range (IQR: defined as the difference between the 75th and 25th percentiles), the topmost and bottom-most horizontal lines indicate the most extreme points less than 1.5 times the IQR below the 25th or above the 75th percentile, black points indicate outliers, and red points indicate individual values