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. 2022 Jul 8;13:3936. doi: 10.1038/s41467-022-31683-9

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Single-nucleus RNA-seq data of 25,349 cells from nine tumors. The UMAP representation of the data is colored and annotated by the 10 cell populations identified. The four tumor-derived cell lineages are indicated by arrows. b Selected differentially expressed genes for tumor-derived and non-tumor cell populations, including marker genes (bold) that were used to annotate the cell populations, as well as differentially expressed genes discussed in the main text. Neuroepithelial-like tumor cell populations (undifferentiated cells, astrocytes, NPCs, and ependymal cells) express multiple genes coding for components of the WNT signaling pathway, whereas MLCs express high levels of hypoxia- and angiogenesis-related genes, and microglia express pro-inflammatory cytokines. c The UMAP representation is colored by the expression level of several differentially expressed genes that are associated with individual tumor-derived cell populations. d UMAP representation showing the origin (primary/metastasis) of each cell. The mesenchymal-like cell population is mostly associated with metastatic tumors. e Stacked bar chart depicting the proportions of each cell type in each tumor. f RNA velocity stream plot. The inferred cell differentiation trajectories originate in the undifferentiated tumor cell population and are consistent with the four lineages of tumor-derived cells indicated in a. g IL1 (top) and TNF-α (bottom) cell-to-cell signaling networks inferred by CellChat based on differentially expressed genes that code for ligands and receptor/co-receptors. The two networks show abundant pro-inflammatory signaling from microglia onto the tumor cells. h The UMAP representation of the single-nucleus RNA-seq data is colored by the expression level of some of the differentially expressed genes between neuroepithelial- and mesenchymal-like tumor cell populations. The UMAPs depict the expression of SOX2 and CD44 (top), and HIF3A and HIF1A (bottom). i Cell-to-cell WNT and hedgehog signaling networks inferred by CellChat indicating a switch between WNT signaling in neuroepithelial-like tumor cell populations and hedgehog signaling in MLCs. IPCs intermediate progenitor tumor cells, MLCs mesenchymal-like tumor cells, NPCs neural progenitor tumor cells, OPCs oligodendrocyte progenitor cells.