Fig. 1
Transcriptional analysis of 925 paediatric nervous system tumours (pedNST) reveals four distinct immune clusters. A Overview of cohorts and sample size in the present study (PDX: patient-derived xenografts, ETMR: embryonal tumour with multilayered rosettes, NFB: neurofibroma, MNG: meningioma, SCHW: schwannoma, CP: choroid plexus tumours, CPH: craniopharyngioma, ATRT: atypical teratoid/rhabdoid tumour, EPN: ependymoma, pedHGG: paediatric high-grade glioma, NBL: neuroblastoma, MB: medulloblastoma, pedLGG: paediatric low-grade glioma). B Distribution of percentage immune reads based on ESTIMATE immune score across paediatric and adult cancers. PDX samples serve as a negative control for immune infiltration. PRAD: prostate adenocarcinoma, LGG: low-grade glioma, OV: ovarian serous cystadenocarcinoma, SKCM: skin cutaneous melanoma, COAD: colorectal adenocarcinoma, GBM: glioblastoma multiforme, LUAD: lung adenocarcinoma. C Heatmap representing consensus clustering using enrichment scores derived from six immune-cell-specific genesets across the pedNST cohort. Cell-type scores correspond to normalized gene set enrichment scores. D Heatmap illustrating proportion of samples in each immune cluster across cancer entities. Barplots show the total number of samples for each row (cancer type) and column (immune cluster). E Heatmap showing fraction of samples in each CRI-iAtlas cluster across immune clusters in pedNST. Barplot shows the total number of samples in each CRI-iAtlas cluster. F Boxplot showing average tumour-infiltrating lymphocyte (TIL) scores as determined by segmentation analysis of pathological images across the paediatric CNS tumour samples (CBTN). Three sample images are shown representing 1% (bottom), 10% (middle) and 15% (top) TIL scores corresponding to lower quartile, mean and higher quartile, respectively. Boxes show median and interquartile range (IQR) and whiskers represent 1.5 times IQR. Two-sided rank sum test, *p < 0.05. G Barplots showing frequency (top barplot) and fraction (stacked barplot) of tumour subtypes across immune clusters (SHH: Sonic Hedgehog, TYR: Tyrosine, MYCN-NA: MYCN non-amplified, MYCN-A: MYCN amplified, WT: wildtype)