Using In Silico And In Vitro Tools To Discover Drivers Of Sensitivity To Novel Cancer Therapeutics
Our client developed a family of compounds that were effective at stopping the growth of tumors in animal models. Although the founding compound had a known target, second generation chemistries had improved therapeutic indices but no longer hit the expected target. Therefore, identifying the target and the mechanism of action of the compounds was critical for moving the compound through the development pipeline and into the clinic. The client had previously tested the lead compound on several hundred cancer cell lines in vitro and determined that some types of cancer were acutely sensitive to drug treatment, while others were completely resistant. Our collaboration with the client was designed to answer the following questions:
- Do gene mutation status or basal gene expression levels correlate with sensitivity or resistance to compound?
- Can the transcriptional response of a sensitive cancer cell line to treatment with the compound reveal the molecular mechanism of action?
- Does modulation of the identified genes confer sensitivity or resistance to compound in vitro?
- Use publicly available cancer cell line basal transcriptional data sets to determine a set of genes that are correlated with the response to the client’s compounds (genome wide association study methods)
- Treat a sensitive cancer cell line with compound and perform next generation sequencing
- Use our proprietary bioinformatic workflows to determine which genes and pathway expression patterns (i.e., molecular endpoints) correspond with sensitivity to the compound
- Use cell-based assays and phenotypic endpoints to determine whether the candidate genes identified were in fact mediating the response to compound
Results from our Work
- A set of predictor genes was identified that correlated with the phenotypic response of cell lines upon exposure to the client’s compounds
- Whole transcriptome analysis of a sensitive cell line identified candidate genes that correlated with response to the compound
- One gene (“Gene X”) had consistently lower expression in sensitive cell lines
- Modulation of Gene X in vitro altered the cellular response to compound:
- Overexpression of the gene in sensitive cell lines conferred resistance
- Deletion of the gene in resistant cell lines conferred sensitivity
- Identification of a gene that was critical for response to compound had two significant benefits:
- Shed light on the molecular pathway that was responsible for compound efficacy and allowed for further investigation of the downstream effects of the compound
- Provided a potential biomarker for identifying a patient population that would benefit from the drug treatment, which would allow for targeted clinical trials to improve the likelihood of success in the clinic