Extended Data Fig. 6: Inflammatory and interferon-stimulated genes suppressed by IL-10 are IRF1/5 targets.
a, b, mRNA of indicated IFN-response genes (CXCL10 and ISG15) (a) and b, inflammatory genes (TNF and IL6) was measured by qPCR and normalized relative to GAPDH mRNA. This analysis was conducted after CRISPR-Cas9 gRNA targeting of IRF1 + IRF5 or HPRT-control for 48 h, followed by stimulation with LPS for 3 h (n = 13 independent donors, some donors are same as Fig. 7a, b). Data are depicted as mean ± SEM. ****p < 0.0001 by Mann-Whitney two-sided test. c–h, Additional analysis of RNA-seq data shown in Fig. 7 obtained using monocytes from 3 independent donors and treated as depicted in Extended Data Fig. 1a. c, PCA plot depicting the RNA-seq data from primary human monocytes subjected to CRISPR-Cas9-mediated deletion of IRF1/5 or HPRT, followed by stimulation with LPS for 3 h. d, k-means clustering analysis (k = 6) conducted on z-score normalized data of differentially upregulated genes in any pairwise comparison relative to resting control. e, Hallmark pathway enrichment analyses performed on clusters identified in d. f, Scatterplot of LPS-induced genes showing log2 fold change values for HPRT-edited and IRF1/5-edited monocytes relative to resting control. g, Venn diagram of LPS-induced genes in HPRT-edited controls compared to IRF1/5-edited monocytes. h, UpSet plot showing interaction between suppressed genes identified in g to individual k-means clusters from d. Created in https://BioRender.com.
