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. Author manuscript; available in PMC: 2020 Jan 1.
Published in final edited form as: Nat Immunol. 2019 Jul 1;20(8):1071–1082. doi: 10.1038/s41590-019-0419-9

Figure 7. SLE DN2 B cells display activation of ATF3-regulated stress response pathways.

Figure 7.

(a) Scatter plot of PageRank fold change between SLE DN2 and HC DN2 versus the gene expression changes for the same comparison. (b) Bar plot of gene expression levels for ATF3 Data represent mean ±SD. * indicates DEG between SLE and HC (>=2-fold change and FDR < 0.05) as determined by edgeR. (c) qRT-PCR analysis of ATF3 in rN B cells from an independent cohort of HC (n = 15) and SLE (n = 8). Data represent mean ±SD and are normalized to percentage of ACTB expression. Significance determined by two-tailed Student’s t-test. (d) Flow cytometry of ATF3 expression compared to isotype control in a representative HC and SLE DN2 B cell sample. The experiment was performed once from a cohort of HC (n = 5) and SLE (n = 8) subjects. (e) ATF3 MFI normalized to isotype MFI for the indicated cell type for a cohort of HC and SLE subjects defined in e. Data represent mean ±SD. Significance determined by Wilcoxon rank sum test. (f) Heatmap of gene expression for 98 genes with ATF3 binding motifs determined by PageRank analysis. Data represent the mean for each cell type. (g) Histogram of ATF3 motif accessibility in HC and SLE cells types. The location of the ATF3 motif is indicated. (h) Box plot for each cell type (right) summarizing accessibility at ATF3 motifs enriched in SLE DN2 DAR. * P-value < 0.05 compared to all other cell types as determined by two-tailed Student’s t-test. Boxplot center line indicates data median, lower and upper bounds of boxes the 1st and 3rd quartile ranges, and whiskers the upper and lower ranges of the data. (i) Network diagram depicting gene sets from Fig. 6b that are regulated by ATF3. Line thickness is scaled to significance as determined by Fisher’s Exact test.