Human DNA-PK activates a STING-independent DNA sensing pathway

Katelyn Burleigh; Joanna H. Maltbaek; Stephanie Cambier; Richard Green; Michael Gale; Richard C. James; Daniel B. Stetson

doi:10.1126/sciimmunol.aba4219

Figure 5:

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The DNA-PK SIDSP activates a broad gene expression program

(A) Heat map representation of log2 Fold Change in gene expression for the 124 antiviral response genes with significant differential expression in one of the four comparisons. The key includes a histogram in cyan plotting the distribution of log2 Fold Change values for all the included genes. Data represent the average of three independent treatments per condition. (B) Expression data for all interferon genes significantly induced in clonal lines of H1 control targeted or STING KO U937 cells, plotting the log2 Fold Change at 8 and 16 hours post treatment. Data represent the average of three independent treatments per condition. (C) To measure the trajectories of global gene expression from 8 to 16 hours post CT DNA transfection, the fold change in gene expression at 16 hours was divided by the fold change for the same genes at 8 hours and plotted for all upregulated genes in STING KO (n=926) and H1 control lines (n=563). ****:p<0.0001, Mann-Whitney unpaired t-test. Data represent the average of three independent treatments per condition. (D) In H1 control U937 cells, the 16 hour CT DNA-activated log2 Fold Change was plotted for DMSO control-treated cells on the x-axis and for Nu-7441-treated cells on the y-axis. Each dot represents a single gene that was differentially expressed at 16 hours in DMSO-treated cells (n=1024). The red line through the origin indicates the line of equivalence representing no effect of the drug treatment. A Wilcoxon matched pairs signed rank test was used to determine the p-value between DMSO control and Nu-7441-treated samples after DNA stimulation. Data represent the average of three independent treatments per condition. (E) In STING KO U937 cells, the effect of Nu-7441 on global gene expression for 1327 genes differentially expressed in DMSO control-treated cells, plotted as in (D). A Wilcoxon matched pairs signed rank test was used to determine the p value between DMSO control and Nu-7441-treated samples after DNA stimulation. Data represent the average of three independent treatments per condition. (F) In STING KO U937 cells, the log2 Fold Change in DMSO control-treated cells was plotted on the y-axis for differentially expressed genes, and the effect of Nu-7441 on these same genes was plotted in log10 format on the x-axis, n=1327. Data represent the average of three independent treatments per condition, each processed and sequenced independently.