I-Corps: Translation Potential of Deep Mutational Scanning with Duplex Sequencing for Evaluating New Drugs to Combat Cancer

The broader impact of this I-Corps project is based on the development of an improved procedure to evaluate preclinical, targeted cancer drugs. Cancer remains a global health concern, with substantial resources being allocated to the discovery and development of next generation anticancer therapies. While mutational scanning has been performed in academic labs, this project will evaluate the commercial potential of a drug screening platform as a service to pharmaceutical companies. There are currently no commercially available services that can profile a compound and successfully predict clinical drug resistance with high accuracy. Comprehensive profiling of investigational drugs at the preclinical stage of development will aid in the design and selection of promising compounds, ideally resulting in more successful clinical trials and accelerating the speed with which better cures for cancer are made available to patients. This I-Corps project utilizes experiential learning coupled with a first-hand investigation of the industry ecosystem to assess the translation potential of the technology. The solution is based on the development of Deep Mutational Scanning with Duplex Sequencing (DMS-DS), a technology that can comprehensively map the mutational landscape of investigational anti-cancer compounds and predict clinical drug resistance in cancer. DMS-DS overcomes the limitations of existing methods for scanning drug resistance by directly measuring the effect of every potential point mutation within the drug target in a quantifiable and translatable way. With this solution, the specific clinical exposure levels required to counteract resistance mutations can be assessed, thereby informing critical dosing decisions during clinical trials. A proof-of-concept was developed and validated using a DMS-DS drug screening platform for BCR-ABL, a genetic test that looks for an abnormal gene that is linked to certain types of blood cancer. The process used duplex sequencing to evaluate a modular BCR-ABL kinase library treated with a compound of interest administered at a clinically relevant concentration. DMS-DS successfully identified all clinically known imatinib resistant mutations and classified 18 variants of uncertain drug resistance with >98% accuracy and a detection limit below 1 in 10,000 cells. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.