Fig. 6

Analysis of immune-cell subtypes in Paediatric Inflamed and Myeloid Predominant provides insights into mechanisms of immunosuppression. A Heatmap showing scaled gene set enrichment scores for 40 T-cell subtypes as annotated in [60] in the Paediatric Inflamed (Tn: Naïve T-cells, Th: T helper, ISG: Interferon-stimulated genes, Tm: memory T-cells, Trm: Tissue-resident memory T-cells, Tem: effector memory T-cells, Temra: effector memory re-expressing CD45RA T-cells, Treg: regulatory T-cells, Tfh: follicular helper T-cells, Th17: T helper 17, Tex: exhausted T-cells, KIR: Killer immunoglobulin-like receptor). B Boxplots showing log-transformed TCRβ estimated Shannon diversity (left) and TMB (right) across T-cell groups (TG). Pairwise two-sided Student’s t test with Bonferroni correction, *p < 0.05, **p < 0.01 and ***p < 0.001 (left). Two-sided rank sum test, *p < 0.05 (right). C Boxplots showing differences in immune-cell infiltration, as determined in Fig. 1C, across T-cell groups (TG). Pairwise two-sided Student’s t test with Bonferroni correction, *p < 0.05, **p < 0.01 and ***p < 0.001. D Heatmap illustrating median tumour-type normalized expression of selected genes in TG2 and TG5. E Heatmap depicting scaled gene set enrichment scores for 9 myeloid cell subtypes as annotated in [61, 104] (DC: dendritic cell, Mono: monocyte, Mac/Macro: macrophage, TAM: tumour-associated macrophage). F Heatmap showing scaled gene set enrichment scores for microglia [62, 63] in the pedCNS subset of Myeloid Predominant. G Heatmap illustrating median tumour-type normalized expression of selected genes in MG1, MG3 and MG5. In all boxplots, boxes show median and IQR and whiskers represent 1.5 times IQR