Genomics for Precision Oncology

The genomics of drug response in ovarian cancer

In collaboration with clinicians and scientists at UAB, the Sara Cooper Lab has used gene expression to characterize patterns that can be used to predict a patient’s response to chemotherapeutic drugs. Our ongoing work explores a variety of applications for gene expression profiling in ovarian cancer including diagnosis, prognosis and response to common therapies. We are particularly interested in using this method to predict response to immunotherapy and have applied methods for profiling RNA derived from the immune system to help assess this response in both animal models and human patients. Our goal is to develop tests that can be use to help direct patient therapy and to propose novel targets that might be relevant for improving response to existing therapies.

Prognostic predictions in pancreatic cancer

A long-term collaboration between the S. Cooper Lab, Myers Lab (also at HudsonAlpha) and investigators at the University of Alabama Birmingham led to the identification of a gene expression signature that can be used to predict patient prognosis in pancreatic cancer (Kirby et al 2016). Continued work in the lab is focused on applying this signature in a clinical setting. We also are characterizing one gene, ANGPTL4. This gene represents a putative drug target given that it is associated both with patient survival and drug resistance in vitro.

Genomic approaches to identification of drug resistance in pancreatic cancer

Using genome-wide CRISPR screening methods, we are identifying genes associated with resistance to chemotherapy in pancreatic cancer cells. Overlapping drug-resistance genes with survival-associated genes reveals known and novel mechanisms for drug resistance. We are interested both in the application of this knowledge to clinical care as well as the study of how these mechanisms arise in pancreatic cancer.