Journal: bioRxiv
Article Title: Pan-cancer tumor classification by a holistic tumor microenvironment atlas
doi: 10.64898/2025.12.27.696641
Figure Lengend Snippet: a, GO enrichment analysis on genes differentially expressed in CXCL9 + and IFIT1 + TAMs. Red and blue represent pathways enriched in CXCL9 + and IFIT1 + TAMs, respectively. P values are adjusted by BH in the hypergeometric test. b, Dot plot showing the expression of representative signature genes of CXCL9 + and IFIT1 + TAMs. The dot size represents the proportion of expressing cells. The color indicates the average level of gene expression. c, Quantification of the mRNA expression of CXCL9 + macrophage-specific gene ( CXCL9 ) and IFIT1 + macrophage-specific genes ( IFIT1 ) in monocyte-derived macrophages, following a 24h stimulation with IFNA1, IFNA13, IFNA14, IFNB1, IFNG or control. P values are calculated using the two-sided t-test, where * indicates P < 0.05, ** indicates P < 0.01, and *** indicates P < 0.001. d, ATAC-seq tracks showing the chromatin accessibility in the CXCL9 and IFIT1 loci for macrophage subsets in TNBC tumors. e, Scatter plots showing the spatial distribution pattern of CD68 + CD163 + CXCL9 + cells and CD68 + CD163 + IFIT1 + cells in representative Xenium samples. Each dot represents an individual cell, and color represents the cell identity. The right bar plots showing the proportion of IFIT1 + or CXCL9 + macrophages across Xenium samples. f, Scatter plots showing effect sizes of the cancer cell state comparisons between c68-CXCL9 high versus c68-CXCL9 low and c69-IFIT1 high versus c69-IFIT1 low tumors. Left: recurrent cancer gene programs (Barkley et al.); right: HALLMARK pathways (MsigDB). Dots represent cancer cell states, and colors represent statistical significance categories. Effect sizes are calculated as Hedge’s g values derived from Student’s t-test, and P values are adjusted by the BH-method. Dots with a BH-adjusted P value < 0.05 and an absolute effect size >0.2 are highlighted.
Article Snippet: Recombinant proteins IFNA1 (Novoprotein, CC75), IFNA13 (MedChemExpress, HY-P72796), IFNA14 (MedChemExpress, HY-P72243), IFNB1 (PeproTech, 300-02BC), and IFNG (PeproTech, 300-02) were then added to the medium at a final concentration of 20 ng/mL.
Techniques: Expressing, Gene Expression, Derivative Assay, Control
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