Fig. 6. miR-126^high gene signature identifies a subset of chemotherapy-resilient LSCs enriched in refractory and relapsed AML.

A Mapping of 126High signature on UMAP plots of NPM1^mut (top, n = 32,194 cells) or del(7) (bottom, n = 21,650 cells) AML cells at diagnosis. B Violin plots of 126High signature expression at diagnosis for each patient, colored by treatment response (dark red: primary refractory, orange: early relapse, green: persistent CR). Percent of cells with 126High > 0 are reported below each violin plot. C Kaplan–Meier plot for overall survival of AML patients within the training (GSE12417 n = 240 and GSE37642 n = 527 newly diagnosed AML patients) and testing (OSHU) gene expression datasets. Log rank test p-value and Cox’s proportional hazards model with lasso penalty hazard ratios (HR) with 95% confidence interval are reported. Red line: 126High signature > median; black line: 126High signature ≤ median. D Top-left: UMAP plot of LSC subclusters colored by unsupervised clustering at resolution = 0.6. Bottom-left: Violin plot of 126High module scores within LSC subclusters. Right: Density UMAP plot of LSCs at diagnosis grouped by outcome categories (green: persistent CR, orange: early relapse, dark red: primary refractory) or at sampled timepoints (diagnosis, Day 14 and Day 30). E Expression of the top 10 marker genes for LSC subcluster 6′ from the PDX scRNAseq dataset, HSC latency genes and 126High signature across NPM1^mut AML LSC subclusters (0″, 1″, 2″ 3″, 4″ and 5″). Dot size represents the percentage of cells expressing the queried gene (columns), color scale represents relative gene expression within the subclusters (rows). F Same as E for del(7) AML LSC clusters (0, 1, 5, 9 and 10). G 126High signature module score distribution within a balanced pool of AML blasts at diagnosis from all non- refractory patients (non Ref. AML – DX), in paired DX-relapse (REL) -post-reinduction (REL NR) samples from PT08, in paired DX-REL samples from PT15 and in REL samples from PT19 and PT20. H Predicted cell cycle phase distribution within sequenced AML blasts grouped by 126High signature expression (126High > 0 POS, 126High ≤ 0 NEG) in DX, REL or REL NR samples from the indicated patients. I GSEA on DEG between REL and DX (left) or REL NR and REL (right) in NPM1^mut AML blasts assigned to the indicated clusters (cl., see for unsupervised clustering). The tile plot shows the normalized enrichment scores (NES), where rows are hallmark terms and columns represent single-cluster, single-patient comparisons between the specified timepoints. Hallmarks (rows) are grouped by semantic similarity. Columns are grouped by cluster phenotype (P, progenitor blasts; E, erythroid-like; C, cycling; M, myelo/monoblasts) and timepoint. Non-significant enrichment results are plotted in light grey (adjusted p > 0.1). J Top: UMAP density projection of blasts at relapse (blue) or diagnosis (grey) on the NPM1^mut AML landscape for PT15. Bottom: UMAP density projection of blasts at relapse (blue), relapse refractory to reinduction (dark blue), or diagnosis (grey) on the NPM1^mut AML landscape for PT08.