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

Journal: Experimental and Therapeutic Medicine

Article Title: TlR2 and TlR4 are involved in the treatment of rheumatoid arthritis synovial fibroblasts with a medicated serum of asarinin through inhibition of T h 1/T h 17 cytokines

doi: 10.3892/etm.2020.8557

Figure Lengend Snippet: Effect of asarinin on cytokine expression of rheumatoid synoviocytes. (A) Left: Fibroblast-like synovial cell morphology of third generation osteoarthritic synoviocytes. Right: third generation of the fibroblast-like synovial cell morphology of rheumatoid synoviocytes (magnification, x40). (B) Changes in the expression of IL-17A, TNF-α, IFN-γ and IL-6 were determined by performing reverse transcription-quantitative PCR. (C) Protein expression of cytokines in rheumatoid synoviocytes. Upper panel: Expression of IL-17A, TNF-α, IFN-γ and IL-6 was analyzed using western blotting with β-actin as a loading control. Lower panel: Density histogram data from three separate western blot analyses (mean ± standard deviation), which represent the relative expression of IL-17A, TNF-α, IFN-γ and IL-6. (D) Quantitative analyses of IL-17A, TNF-α, IFN-γ and IL-6 using ELISA. * P<0.05 and ** P<0.01 vs . control cells. IL, interleukin; TNF, tumor necrosis factor; IFN, interferon; RASF, rheumatoid arthritis synovial fibroblast; OASF, osteoarthritis synovial fibroblast.

Article Snippet: The ELISA kit for IL-17A (cat. no. D1700) was obtained from R&D Systems, Inc. Primary antibodies for TNF-α (cat. no. TA808184), IL-17A (cat. no. TA337063), IL-6 (cat. no. TA500067) and IFN-γ (cat. no. TA353236) were from OriGene Technologies, Inc. Peptidoglycan (PGN) and lipopolysaccharide (LPS) were purchased from Sigma-Aldrich.

Techniques: Expressing, Real-time Polymerase Chain Reaction, Western Blot, Standard Deviation, Enzyme-linked Immunosorbent Assay