Table 1.
Fold change in IFN antiviral EC50 values for shUSP18 stable cell lines
Cell line | % USP18 expression (95% confidence limit)a | HCVcc assay |
HCV replicon |
EMCV assay |
|||
---|---|---|---|---|---|---|---|
FC in IFN antiviral potency (95% confidence limit)b | P value | FC in IFN antiviral potency (95% confidence limit)b | P value | FC in IFN antiviral potency (95% confidence limit)b | P value | ||
Control | 70.4 (63–77) | 1.1 (0.5–2.1) | 0.90 | 0.7 (0.4–1.3) | 0.29 | 0.7 (0.3–1.4) | 0.26 |
shUSP18a | 13.9 (11–17) | 2.9 (1.4–5.7) | 0.003 | 2.9 (1.5–5.7) | 0.002 | 2.6 (1.3–5.1) | 0.0076 |
shUSP18b | 49.4 (37–62) | 1.4 (0.7–3.0) | 0.37 | 0.7 (0.3–1.5) | 0.33 | 0.7 (0.4–1.4) | 0.32 |
shUSP18c | 10.9 (8–14) | 1.1 (0.6–2.2) | 0.73 | 1.4 (0.8–2.6) | 0.25 | 0.9 (0.5–1.8) | 0.77 |
shUSP18d | 16.5 (10–23) | 1 (0.5–2.1) | 1.00 | 2.9 (1.5–5.6) | 0.002 | 0.4 (0.2–0.8) | 0.013 |
The USP18 mRNA levels were assayed by using RT-PCR, and values were corrected for actin expression by adjusting the USP18 arbitrary copy number in each well by the relative amount of actin present. The corrected values were then normalized to the nontransfected cell control to give the percent expression (percent USP18). Values from Huh7.5 cells (n = 2), Huh7 cells (n = 1), and HeLa cells (n = 4) were averaged, and the 95% confidence limits are given in parentheses.
The fold change (FC) is the difference in EC50s between the nontargeting shRNA control stable cells and USP18 shRNA stable cell line (note that the control FC values were calculated relative to nontransfected cells). The FC values and probabilities were calculated by generating control test pairwise comparisons The shUSP18 IFN EC50s were analyzed on the logarithmic scale by using a linear mixed model, comparing the nontargeting shRNA control stable cells and USP18 shRNA stable test cell lines within each assay type and accounting for experimental variation. The comparisons were summarized with FC values, 95% confidence limits (in parentheses), and P values.