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. 2022 Jun 24;13:3606. doi: 10.1038/s41467-022-31340-1

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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. 4 — A (a) Schematic representation of spatial transcriptomic analysis of glioma oncostreams using Laser Capture Microdissection (LCM). Glioma tumors were generated by intracranial implantation of NPA tumor cells in C57BL6 mice (Created in BioRender.com). (b, c) Oncostream areas (red outline) were identified and dissected from surrounding glioma tissue (black outline) of three independent mouse tumor samples using a LCM microscope. Scale bar: 100 μm. B A volcano plot displays differentially expressed (DE) genes from oncostream vs no-oncostream areas. DE genes were selected based on a fold change of ≥ 1.5 and a q-value (false discovery rate (FDR) corrected p-value) of ≤ 0.05. Two-sided multiple t-test. Upregulated genes (red dots) and downregulated genes (blue dots) are shown. Relevant genes related to mesenchymal migration are labeled on the graph (n = 3, biologically independent replicates per group). C Heat map illustrates gene expression patterns for oncostream vs no-oncostream areas in NPA glioma tumors (n = 3, biologically independent replicates per group). Differentially upregulated genes (16) are represented in red and downregulated genes (n = 27) are represented in blue (q-value ≤ 0.05 and fold change ≥ ± 1.5). D Functional enrichment analysis of overrepresented Gene Ontologies (GO) terms (biological processes) obtained when comparing oncostream vs no-oncostream DE genes. p-value corrected for multiple comparisons using the FDR method. Cutoff FDR < 0.05. Blue: Downregulated GOs. Red: Upregulated GOs. E Bar graphs show DE genes annotated to the most relevant enriched GOs biological process. Upregulated genes (red), downregulated genes are (blue). Biologically independent replicates (n = 3) per group. Box and whisker plot on the left summarizes the distribution of differentially expressed genes. center line of the boxplot (median), upper bound of the boxplot is the Q3 (75th percentile), the lower bound of the boxplot is the Q1(25th percentile), the upper whiskers is the maximum value of the data (within 1.5 times the interquartile range over the 75th percentile), and the lower whisker is the minimum value of the data (within 1.5 times the interquartile range under the 25th percentile). Outliers are represented by circles. The Data (D, E) were analyzed using Advaita Bio’s iPathwayGuide.