Fig. 4

Gene expression profiles. A Change in Gene Set Variation Analysis (GSVA) scores showing relative enrichment of the indicated STAT3 or IL-6-related pathways in post-run-in samples compared to pre-run-in. B GSVA score used in A for the Hallmark IL-6 STAT3 signaling pathway in pre-run-in and post-run-in patient biopsies. C Dot plots depicting the comparison of post-run-in to pre-run-in signature enrichment alterations between patients receiving RUX (n = 4) and RUX + PAC (n = 4) treatments. Nine JAK-STAT-related (left) and six IL6-related signatures (right) were plotted separately. D Pearson correlation values and significance for indicated gene signature enrichment in post-run-in compared to pre-run-in as determined by RNA-seq and change in pSTAT3 levels as assessed by indicated staining method. E Heatmap depicting log2 fold change expression values of indicated genes in post-run-in compared to pre-run-in. F Delta GSVA scores for gene set enrichment analysis on patient samples treated with RUX (n = 4) or RUX + PAC (n = 4) during run-in. G GSVA score showing enrichment of the Hallmark EMT pathway in pre-run-in or post-run-in samples. H Changes of immune cell subtype abundance in post-run-in samples compared to pre-run-in. I Line plot illustrating the changes of M0/M1 macrophages ratios in post-run-in samples compared to pre-run-in. J Changes in overall numbers of BCR and TCR clonotypes in post-run-in samples compared to pre-run-in. K BCR diversity (True Diversity Index) changes in post-run-in samples compared to pre-run-in in RUX and RUX + PAC treatment groups. Two-sided paired students’ t test (for C, G, J, K) and Wilcoxon matched-pairs signed rank test (for I) between pre-run in and post-run-in samples were used, respectively