Fig. 2

Quantitative proteome analysis indicates spatially distinct protein signatures. a, b Venn diagram of common and “exclusive” proteins identified for a neoplastic islands or b tumor stroma from the ITF and the inner tumor. c, d Clustering analysis of proteins identified in the ITF and the inner tumor of c neoplastic islands (n = 20 samples) and d tumor stroma (n = 17 samples). Values for each protein (rows) and for each microdissected sample (columns) are colored based on the protein abundance, in which high (red) and low (blue) values (Z-scored log2 LFQ intensity values) are indicated based in the color scale bar shown in the top left of the figure. The colored bars shown on the top of the figure indicate samples from the ITF (blue) or from inner tumor (pink). Hierarchical clustering was performed in the R environment using the Euclidean distance with complete ligation for neoplastic island data and the Euclidean distance with average ligation for stromal data. e, f Heat map of Pearson correlation coefficients derived from pairwise comparison of the 20-patient samples for e neoplastic island samples and for the f tumor stroma samples analyzed by discovery proteomics. Log2 LFQ intensity values of the protein dataset after filtering reverse and “only by site” entries were used to calculate the correlation coefficient using Perseus software, and the heat map was constructed using R language with the function heatmap.3. The dendrogram was built using Euclidean distance with complete ligation. Samples with low correlation values and low number of quantified proteins from tumor stroma dataset were removed, as shown in Supplementary Figure 2. g The five most enriched GO terms that distinguished neoplastic islands from tumor stroma are represented. GO terms for cellular metabolic processes are overrepresented for neoplastic island proteins, whereas cellular adhesion and protein cleavage processes are overrepresented for tumor stromal proteins. The statistically significant proteins between neoplastic islands compared with tumor stroma (two-sided Student’s t test, P value < 0.05) also indicate, among other overrepresented processes, metabolic processes for proteins upregulated in neoplastic islands