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To tailor cancer treatment: Study uses computer simulation to model patient cancer DNA

UF Health researcher Jatinder Lamba, Ph.D., UF Health physician and researcher Christopher Cogle, M.D., and co-founder of Cellworks Group Inc. Taher Abbasi discuss a clinical trial that will examine whether computer simulation modeling can accurately predict how a person reacts to the different cancer therapies that their doctor has prescribed, depending on the person’s genes. Recently, President Barack Obama unveiled the Precision Medicine Initiative, a program that fosters a research approach focusing on treating patients based on their genetic makeup.

At University of Florida Health, researchers launched a clinical trial that tests a new method of translating thousands of gene mutations into treatment options for patients. Using computer simulation modeling, the researchers will examine if the computer program will accurately predict how a person reacts to the different cancer therapies that their doctor has prescribed, depending on the person’s genes. Not only will the software take the genes of a patient’s cancer into account, it will also examine the genes that govern how a person reacts to a particular medication.

UF Health physician and researcher Christopher Cogle, M.D., lead investigator of a clinical trial that will study the effectiveness of this computer model, treats and studies different types of blood cancers and typically sees patients whose cancer has relapsed. To determine the best course of treatment for individual patients, Cogle needs to map thousands of genes within each patient’s cancer that can drive aggressive growth. Cancer often involves hundreds to thousands of gene abnormalities, which raises one of the most difficult challenges in medicine: how to decode the numerous DNA misspellings that drive disease.

Cogle is teaming up with Jatinder Lamba, Ph.D., a member of the UF Genetics Institute, the UF College of Pharmacy and a cancer pharmacogenomics researcher, an area of research preeminence. Together, they will examine 91 genes involved in the movement of drugs within the body. These so-called “pharma-genes” will then be tested to identify which treatments are safest and most effective for the patient.

“The cancer genes are genes we believe will give us prognostic and treatment information, and the pharma-genes will tell us how well the patients will respond to the drugs we prescribe,” said Cogle, a member of the UF Health Cancer Center and an associate professor of medicine in the UF College of Medicine’s department of medicine.

This kind of close examination is a new approach to cancer treatment, taking into account not only how well a therapy targets cancer, but also how that therapy impacts the health of a patient. Typically, to find the significance of a cancer mutation, cancer doctors use a manual approach through PubMed, a free search engine overseen by the National Institutes of Health that catalogues studies in life sciences and biomedicine. But searching for one gene, a medication to treat it, and how that medication might react in a person’s body could take hours, Cogle said.

That’s where Cellworks Group Inc., a California-based company, comes in. The company created a simulation technology to generate a computer model of each person’s cancer. Cellworks can then model how the cancer responds to standard chemotherapies.

“Think of the simulation as a map of a city. Hypothetically, if you have a major highway and intersections, you could predict what happened in a model of that traffic map by inputting different traffic situations. It’s the same with patients: The model is basically an internal map of all of these processes happening inside the body,” Cogle said.

If the computer method is proven valid, this prediction technology could help doctors and patients both choose drugs with greatest likelihood of shrinking the cancer and avoid harmful drugs with low chance of success. For patients who aren’t responding to standard chemotherapy and for patients whose cancer has relapsed, each patient’s computer model could be used to search for other FDA-approved drugs that may be more effective.

Agilent Technologies, a California-based company, will provide state-of-the-art tools to measure DNA taken from patients at UF Health.

“We’re interested in supporting and being part of this effort because the program at UF Health, together with Agilent and Cellworks, is a way to test a potentially transformational approach to thinking about diagnostic and therapeutic selection for cancer treatment,” said Darlene Solomon, Ph.D., chief technology officer and senior vice president of Agilent Technologies.

For UF Health researchers, that means first developing accurate and precise tools for predicting cancer shrinkage and side effects. Their ultimate goal is to ensure that individual patients are matched to tailored treatments that best treats their cancer and causes the least amount of harm.

“Each patient should receive a therapy that’s best for that patient — that’s what we’re trying to do,” Lamba said.

The clinical study launched in June 2015.

About the Author

Morgan Sherburne's picture

Morgan Sherburne

Science Writer

Science writer for UF Health. Morgan writes about the research of faculty physicians in the College of Medicine. She joined the UF Health staff in 2014. A Michigan native, she...Read More

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