Figure 5.
AHR activity controls IL-10-induced gene expression patterns
(A) Ratio of the indicated transcripts in molecules/μL to HPRT molecules/μL in arbitrary units (a.u.) by ddPCR in DC-10s and AHRinhDC-10s.
(B and C) Volcano plots of differentially accessible regions (DARs) by ATAC-seq (B) and differentially expressed genes (DEGs) by RNA-seq (C) in DC-10s and AHRinhDC-10s.
(B) Horizontal line at p = 0.01. Vertical line at logFC = 1. Gray dots = peaks obtained from the DC-10 vs. AHRinhDC-10 analysis; black dots = 107 DC-10-specific enhancers obtained in the DC-10 vs. DC analysis (see Figure 1D), the number of DC-10-specific enhancers enriched in DC-10 and AHRinhDC-10 peaks (p < 0.05) is indicated; pink dots = peaks accessible in DC-10s and not in AHRinhDC-10s. p value by Fisher’s exact test. The number of DARs in the two conditions is indicated.
(C) Gray dots = non-differential genes; Red dots = DEGs (p < 0.01). Ten most significant DEGs in each group are indicated.
(D) GSEA of the 91 DC-10 core genes in the AHRinhDC-10 vs. DC-10 transcriptomes. Normalized enrichment score (NES) and FDR q-value are indicated.
(E) NES (y axis) and FDR q-value (dot size, expressed as -Log10) by GSEA of gene sets upregulated (red bubbles) and downregulated (yellow bubbles) in monocytes upon 24 h of IL-10 exposure (IL-10; GSE59184), in dexamethasone-induced (DEX) tolDC42 and in Vitamin D3-induced tolDC (VITD3; GSE13762), assessed in AHRinhDC-10 vs. DC-10 transcriptomes. Blue area = DC-10 enriched, light blue area = AHRinhDC-10 enriched.
(F) IL-10 receptor alpha (IL10RA) expression by ddPCR in DC-10s and AHRinhDC-10s at 2 and 5 days of in vitro differentiation expressed as the ratio of IL-10 molecules/μL to HPRT molecules/μL in arbitrary units (a.u.).
(G) Phosphorylated-STAT3 (p-STAT3) fluorescence intensity (RFI) by flow cytometry (FC) of IL-10-stimulated, relative to -unstimulated, DC-10s, AHRinhDC-10s, and DCs at days 2 and 5 of differentiation. (A, F, and G) p values by Wilcoxon matched pairs test. See Figure S5.