Using transcriptome sequencing to identify mechanisms of drug action and resistance

Selection of clones resistant to drugs in human cells, followed by massively parallel transcriptome sequencing of these clones and bioinformatics analyses to identify genes mutated with high frequency, allow for identification of direct targets and indirect resistance mechanisms of cytotoxic drugs. Determining mechanisms of drug action in human cells remains a major challenge. Here we describe an approach in which multiple-drug-resistant clones are isolated and transcriptome sequencing is used to find mutations in each clone. Further analysis of mutations common to more than one clone can identify a drug's physiological target and indirect resistance mechanisms, as indicated by our proof-of-concept studies of the cytotoxic anticancer drugs BI 2536 and bortezomib.