Systems Study Taps Cancer Gene Expression Reversal to Predict Drug Response

NEW YORK (GenomeWeb) – Drugs that prompt promising anti-cancer responses in preclinical disease models also lead to gene expression shifts in related cell lines that may be useful for predicting drug effectiveness, new research suggests.

“Using gene expression as a representation of the molecular state, a number of studies have demonstrated its potential in drug discovery; yet, there was no systematic way to correlate reversal potency and drug efficacy,” senior author Atul Butte, a researcher at the University of California at San Francisco, and his co-authors wrote in their new Nature Communications study.

“Our study leveraged the emerging public cancer genomics and pharmacogenomics databases to address this challenge,” they explained, “and we successfully demonstrated that reversal potency correlates with drug efficacy and can be used to predict potential new drug candidates for several cancer types.”

As they reported online today, the researchers established cancer-related gene expression signatures based on RNA sequence data for thousands of samples from 14 cancer types that were assessed for the Cancer Genome Atlas project. They considered these signatures in relation to the expression patterns produced when dozens of cell lines were exposed to more than 12,400 drug compounds, uncovering expression changes that seemed to accompany

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