Determining Mode of Action

Purpose:

The purpose of this study was to use gene expression and pathway analysis to determine the mode of action of a drug in a Phase II clinical trial for the treatment of uterine bleeding.

Study Design:

Whole blood samples were obtained from placebo- and drug-treated patients taking part in the 12 week randomised double blind trial for uterine bleeding.

Extracted RNA was hybridised to Affymetrix Human Genome U133 arrays.

The analysis performed included a stringent QC of the arrays, differential gene expression analysis across treatment groups and dose levels, statistical filtering to identify robust markers, network-based clustering and functional pathway analysis and biomarker discovery for confirming the mode of action.

Conclusions

The results showed a strong pattern of down-regulation in a cluster of immune-response genes.

The drug was shown to be effective by modulation of immune response and vascular remodelling by suppression of immune markers IL-55 and CD56.

In addition to the above, a further cluster of modulated genes was identified and found to be involved in development of cancer & apoptosis. Following completion of the study the drug was withdrawn from development.

Implications

The above case study shows that gene expression with associated pathway analysis can be used to both identify the mechanism of action of a compound and also highlight genomic changes which may give rise to side effects following prolonged use.