Fig. 2: Transcriptional differences between immune-infiltrated and immune-depleted pediatric AML.

A Schematic overview of the study population, used techniques, and analyses performed in Fig. 2B–D. B Comparison of the normalized abundance of CD20⁺ B cells in the bone marrow of pediatric AML (CD20 stains available for 69 cases) with CD3⁺ T cell levels above or below the median of non-leukemic controls (later referred to as immune-infiltrated and immune-depleted, respectively; Mann–Whitney test). C Volcano plot of differentially expressed genes between immune-infiltrated (n = 6) and immune-depleted (n = 17) pediatric AML bone marrow biopsies, identified using DEseq2 with an FDR cut-off of 0.05 and minimum fold change (FC) of 2. D Single-sample gene set enrichment analysis of differentially expressed genes between immune-infiltrated and immune-depleted cases using the GO Biological Processes gene set with an FDR cut-off of 0.05. WikiPathways-related results are shown in Table S2. E Schematic overview of the study populations for which gene-expression data was available (primary study cohort and TARGET-AML cohort), and the associated analysis. F Correlation plot of the negative correlation between the M2-predominance score and the normalized number of CD3⁺ T cells, calculated using Spearman correlation. G Comparison of the M2-predominance score between immune-infiltrated (n = 6) and immune-depleted (n = 17) cases using the Mann–Whitney test. H Correlation plot of the negative correlation between the M2-predominance score and the estimated abundance of T cells in the bone marrow of TARGET-AML cases, calculated using Spearman correlation. I Comparison of the M2-predominance score between immune-infiltrated (n = 80) and immune-depleted (n = 79) cases using the Mann–Whitney test.