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. 2023 Apr 12;12:e74913. doi: 10.7554/eLife.74913

Figure 2. The CX3CR1 gene module of CD1c+ DCs is enriched for NOTCH2-RUNX3 signaling.

(A) Volcano plot for the expression of genes of the black module in cDC2s of runx3-KO mice (GSE48590), notch2-KO mice (GSE119242), and type I IFN-dependent inflammatory [inf-]cDC2s (GSE149619). Up- and downregulated genes for each condition are indicated for each condition; gray dots denote the genes with no significant change in expression. (B) Results from gene set enrichment analysis for ranked transcriptomes (using 20,668 genes with baseMean >4) for AU, IU, and BU patients. The top or bottom percentiles of the ranked [−log10(p) × sign(log2(FC))] genes from runx3-KO cDC2s, notch2-KO cDC2s, and inf-cDC2s (see a) were used as gene sets. Normalized enrichment scores (NES) and p values for each gene set are indicated. The dotted lines indicate padj = 0.05. AU: anterior uveitis, IU: intermediate uveitis, BU: birdshot uveitis.

Figure 2.

Figure 2—figure supplement 1. In vitro stimulation of CD1c+ DCs and gene enrichment analysis.

Figure 2—figure supplement 1.

(A) Gene expression (mean [standard error of the mean, SEM]) for RUNX3 and CD36 in primary human CD1c+ DCs from healthy donors stimulated overnight. Each dot represents a single donor used in the experiment. (B) Transcriptomic data (GSE110577, described by Kirkling et al., 2018) of murine bone marrow progenitors cultured for 7 days with OP9 stromal cells that express the NOTCH2 ligand DLL1 or OP-9 cells without DLL1. This analysis revealed that notch2-controlled genes were enriched in the transcriptome of CD1c+ DCs of patients and that notch2-signaling associates with the expression of cd36, ccr2, and cx3cr1 in cDC2s. Normalized counts (and adjusted p values from DESeq2) for cx3cr1, ccr2, cd36, and runx3 from cDC2s generated from murine bone marrow cells and OP-9 with (in blue) or without (in ochre) Notch ligand Delta-like 1 (DLL1). (C) Gene set enrichment analysis using the top 1% (n = 201) genes associated with the NOTCH-negative condition in b as the gene set. R848: Resiquimod, LTA: lipoteichoic acid, LPS: lipopolysaccharides, Pam3CSK4: Pam3CysSerLys4, OxLDL: oxidized low-density lipoprotein, IFNα: interferon alpha, TGFβ: transforming growth factor beta, FLT3L: FMS-like tyrosine kinase 3 ligand, TNFα: tumor necrosis factor alpha, S100A12: S100 calcium-binding protein A12, IL-4: interleukin 4, GM-CSF: granulocyte-macrophage colony-stimulating factor.