Fig. 1: Intratumoral MHC-II⁺ HSPCs in childhood brain tumors.

a, Representative t-distributed stochastic neighbor embedding (t-SNE) of flow cytometry data from developmental time points (embryonic day 12.5 (E12.5), P5, P19 and P49), with 3,000 events concatenated per sample, manually gated (key shown on the right in c). b, Schematic of the flow cytometry approach for characterizing the tumor microenvironment in a de novo ZFTA–RELA fusion ependymoma model. c, t-SNE analysis of 18,000 events from endpoint EP^ZFTA-RELA mice, showing proportions of CD45⁺ cells; M1 microglia, M2 microglia, neutrophils, microglia, monocytes, CD8 T cells, CD4 T cells, macrophages, natural killer cells, B cells, innate lymphoid cells, T_reg cells, γδ T cells, hematopoietic stem cells (HSCs), multipotent progenitor cells and dendritic cells. d, Quantification of LSK⁺ within the CD45⁺ population in EP^ZFTA-RELA and Nestin^CreERT2 control mice (n = 5; mean ± s.e.m.; one-way analysis of variance (ANOVA) with Šídák’s test). e, UMAP of human scRNA-seq data integrated from fetal brain tissue and tumor tissue from patients with childhood brain tumors, colored by cell type annotation: B cells; CD4 tissue central memory cells (T_CM); CD4 tissue effector memory cells (T_EM); CD8 T cells; HSPCs; IFNγ macrophages; IFNγ microglia; natural killer T cells; purinergic receptor P2Y12^low microglia; T_reg cells; conventional dendritic cell types 1 and 2; complement myeloid cells; fetal, infantile and resting microglia; monocytes; neutrophils; and proinflammatory macrophages and microglia. f, Quantification of proportions of cell types across each disease group; anaplastic astrocytoma, anaplastic glioma, diffuse intrinsic pontine glioma, group 3 (Gr3) and group 4 (Gr4) medulloblastoma (MB), posterior fossa type A (PFA) ependymoma types 1 and 2, posterior fossa type B (PFB) ependymoma, sonic hedgehog (SHH) medulloblastoma, supratentorial-REL-associated protein (ST-RELA) ependymoma (EPN), ST-Yes1 associated transcriptional regulator (YAP) EPN. g, Tissue UMAP of HSPC clusters in malignant and nonmalignant brain tissue, colored by cell type annotation: common lymphoid progenitor (CLP), common myeloid progenitor (CMP), granulocyte–monocyte progenitor (GMP) and HSC. h, Dot plot of average and percentage expression of MHC-II antigen presentation machinery across HSPC cell clusters in malignant and nonmalignant brain. i, Representative histogram of MHC-II cell surface expression for LSK cells, B cells, dendritic cells and CD4 T cells. j, Quantification of proportions of MHC-II expression in intratumoral LSK⁺ relative to LSK⁻ cells (n = 6 per group, mean ± s.e.m., unpaired two-tailed Student’s t-test). a.astrocytoma, anaplastic astrocytoma; a. glioma; anaplastic glioma; BC, B cells; cDC, conventional dendritic cells; DC, dendritic cells; DMG, diffuse intrinsic pontine glioma; ILC, innate lymphoid cells; macro., macrophages; i.v., intravenous; MG, microglia; MPP, multipotent progenitor cells; neutro., neutrophils; NK, natural killer; pro-inflam., proinflammatory; TC, T cells. Illustrations in b created with BioRender.com.