Fig. 4: miR-126^high LSCs co-express stem cell and lymphoid transcriptional profiles and up-regulate inflammatory signaling upon chemotherapy.

A Principal component analysis (PCA) on the top 1000 most variable genes prior to (left) or after batch correction for patient-derived variability (right). Samples are coded for sorted GFP subpopulations (green: GFP^low, grey: GFP^high) and treatment groups (circles: control, triangles: chemotherapy-treated mice). n = 31 PDX from 4 patients. B Enrichment plot of Gene Set Enrichment Analysis (GSEA) of indicated gene lists within DEGs between GFP^low/miR-126^high and GFP^high/miR-126^low blasts. Normalized Enrichment Score (NES) and q-value are reported for each signature. C Heatmap of agglomerated z-scores for selected Gene Ontology—Biological Processes (GO-BP) enriched terms (rows), grouped by semantic similarity, from the comparison of GFP^low/miR-126^high vs. GFP^high/miR-126^low populations in over-representation analysis (ORA). Each column represents a sorted sample. Treatment group, patient ID and GFP population are annotated on top. n = 62 samples from 31 PDX from 4 patients. D Heatmap of agglomerated z-scores for enriched Hallmark gene sets (MSigDB H group) (rows) from the chemotherapy-treated vs. control comparison in GFP^low/miR-126^high blasts only. Each column represents a sorted sample. Treatment group, patient ID and GFP population (GFP^low) are annotated on top. n = 31 samples from 31 PDX from 4 patients. E Heatmap of agglomerated z scores for enriched senescence-associated gene signatures (rows) from the chemotherapy-treated vs. control blast comparison. Each column represents a sorted sample. Treatment group, patient ID and GFP population (GFP^low or GFP^high) are annotated on top. n = as per panel A. Source data are provided as a Source Data file.