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In this independent study group we confirmed the negative correlation between baseline gene expression level and treatment induced biological response (p<0.0085 and R = −0.4719).
This analysis demonstrated that the mean baseline expression of the 28 IFN response genes negatively correlates with the in vivo IFN-induced response levels (p = 0.0049 and R = −0.6657) (Figure 2A), suggesting that the baseline gene expression level of these genes could serve a role as predictive marker for the pharmacological responsiveness to IFNß.
In addition, these constructs are also associated with a low baseline gene expression level allowing the study of genes whose expression may be incompatible with the generation of constitutively expressing clones.
Although pretreatment with either cytokine inhibitor had no effect on the baseline gene expression level of aggrecan in AF cells derived from degenerative tissue, type I collagen baseline gene expression was reduced in these cells.
It is also worth noting that treatment with IL-4RAb had no effect on the baseline gene expression level of MMP3 in AF cells derived from nondegenerative tissue, suggesting that the maintenance of baseline MMP3 gene expression occurs independently of IL-4.
Treatment of AF cells derived from nondegenerative tissue with either cytokine inhibitor IL-1Ra or IL-4RAb had no effect on the baseline gene expression level of ADAMTS4, suggesting that the maintenance of ADAMTS4 baseline gene expression occurs independently of both IL-1 and IL-4.
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To test whether age-dependent differences in the transcriptional program induced by vaccination were associated with altered gene expression levels pre-vaccination, we directly compared baseline gene expression levels in young versus older adults and identified 40 differentially expressed genes (Supplementary Table 2).
Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories.
Geeleher, P., Cox, N. J. & Huang, R. S. Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines.
Comparing baseline gene expression levels and biological response using the average of these 15 genes revealed a significant negative correlation (R =��−0.7208; p = 0.0016) (figure 2B).
Since e.g. IFNα is known to desensitize further responses to IFNs, the presence of low endogenous IFNs could block IFNß-induced signals.[33], [34] This explorative pilot study suggests a predictive value of baseline gene expression levels of IFN-induced genes.
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