Unique gene machine opens new pathways to personalized medicine

In the UAB Nanostring Laboratory, researchers such as Eddy Yang are taking advantage of the nCounter Analysis System's novel digital profiling technology to examine specific signaling pathways in cancer and other diseases. That work could lead to new insights to improve diagnosis and treatment decisions.

Cancer is a devious enemy. In lab tests, researchers have identified plenty of exciting genetic targets — weak links that should allow them to destroy tumors by halting production of a crucial enzyme, for example, or blocking a signal the cell needs to keep growing. All too often, however, these promising findings fizzle out in further testing.

That is because cancer cells can take advantage of multiple, redundant signaling pathways to avoid areas that come under attack. “Tumor cells will just figure out a way to bypass them,” said Eddy Yang, M.D., Ph.D., an associate scientist in the UAB Comprehensive Cancer Center and associate professor in the UAB Department of Radiation Oncology.

Mapping out the complex pathways involved in cancer and other diseases is a crucial step in finding better treatments — and identifying the best treatments for individual patients. If you know all the routes a tumor can use to evade attack, you can find therapies — or combinations of therapies — to block them all. Indeed, tracing cancer-related signaling pathways, and finding ways to use these insights to improve diagnosis and treatment decisions, is a major focus of research at the Cancer Center, Yang says. But spotting these pathways amid the information overload of a genomewide screening test can be extremely complex and time-consuming.

nCounter: In Focus 48-800 genes can be studied simultaneously Applications include gene expression analysis, microRNA and lncRNA analysis, copy number variation analysis, ChIP-String analysis and leukemia fusion gene analysis The system's novel digital technology is based on direct multiplexed quantification of nucleic acids; it provides highly reproducible data over 5 logs of dynamic range Preconstructed panels include: PanCancer Pathways Panel, Human Kinase Panel, Human Immunology Panel, microRNA Panels, Cancer Copy Number Variation Assay See the UAB Nanostring Laboratory site for more information and a schedule of fees and services

Targeting Crucial Pathways

Now, UAB researchers and clinicians have a new tool to investigate signaling pathways — and to translate their discoveries into clinic-ready diagnostic tests. The unique nCounter Analysis System, produced by Nanostring Laboratories, “is a platform to measure the expression of genes in a targeted manner,” Yang said. “Instead of looking at the whole genome, you can investigate anywhere from 48-800 genes at a time.” Researchers can zero in on certain pathways that they are studying, Yang explains, or they can use preset panels of previously identified cancer networks.

Yang directs the new UAB Nanostring Laboratory, which is open to investigators across campus. He is using the nCounter to pursue his own research in experimental treatments for breast, prostate, and head and neck cancers. “I’m very interested in understanding the pathways that make a tumor tick,” Yang said. “I want to know which ones make it resistant to therapy and which ones could actually make it more sensitive to treatment.” With the nCounter, Yang said, “we can look from a 10,000-foot perspective rather than from sea level. It’s an exciting technology.”

Another advantage of the nCounter is that, unlike other technologies, which may require whole molecules of high-quality RNA or amplification for analysis, the nCounter can gather information from small pieces of RNA. That means researchers can use it to look at pathways in tissue that is up to several decades old, retroactively verifying new patterns they have found instead of having to collect new samples for analysis. The nCounter can also perform a range of other tests, Yang says, including analysis of microRNAs, gene fusions and gene amplifications.

From Concept to Clinic

The nCounter is more than a research tool. It can run new diagnostic tests such as the ProSigna Assay, which gives clinicians an estimate of a patient’s likelihood of tumor recurrence based on which pathways are active in that patient. It is an excellent example of personalized medicine in action, Yang says. He envisions UAB researchers using the nCounter to develop novel tests to inform treatment decisions in cancer and other diseases. UAB is one of the first institutions nationwide with the ability to do both laboratory and clinical testing using the nCounter.

“We hope to use the pattern of the pathway of genes to help guide therapy,” Yang said. “That’s the personalized medicine approach.”

Yang and collaborator Andres Forero, M.D., senior scientist at the UAB Cancer Center, will use the nCounter as part of a clinical trial testing a new treatment approach against triple-negative breast cancer. The trial, which recently began enrolling patients, is testing two different drugs — a PARP inhibitor and an EGFR inhibitor — to block two different pathways used by these tumors.

“By blocking PARP, you block the ability of the tumors to repair DNA damage,” which should eventually result in cell death, Yang explains. But the tumors can take advantage of an alternate backup pathway to repair that damage, meaning PARP inhibitors alone are often ineffective. “By blocking EGFR, we will block that backup pathway,” Yang said. [To learn more about this study, call (205) 934-0309; visit the Clinical Trials section of the Comprehensive Cancer Center's website to see all current studies.]

Using the nCounter, the researchers will compare the pathways altered in patients who respond to the therapy with those in patients who aren’t helped by the combination. In the future, that could let them identify the most appropriate patients for this treatment with a simple test. “We hope to use the pattern of the pathway of genes to help guide therapy,” Yang said. “That’s the personalized medicine approach.”

Grad student receives national award for new insight on alcohol and liver damage

Uduak Udoh

By connecting the dots between chronic drinking, molecular clocks, and energy storage patterns, UAB doctoral student Uduak Udoh has identified a potential new approach to target alcoholic liver disease. The work has also earned her a top honor from the Research Society on Alcoholism (RSA) and the National Institute on Alcohol Abuse and Alcoholism (NIAAA), and kudos from former NIAAA director Enoch Gordis, M.D.

Udoh, a fifth-year doctoral student in Pathobiology and Molecular Medicine, received the Enoch Gordis Research Recognition Award during the RSA's annual scientific meeting this summer. At the meeting, she presented results from her dissertation project, "Hepatic Glycogen Metabolism Is Impaired by Alcohol Consumption: Possible Role of the Liver Molecular Clock."

Liver cells, like almost all human cells, have a built-in circadian clock—a set of genes that control metabolism and other biological processes in a daily cycle. Udoh's research shows that chronic alcohol consumption disrupts the liver's normal pattern of creating glycogen, a storage form of glucose.

"Glycogen in the liver is an important fuel reserve that the body uses in between fasting and eating," explains Udoh, who is a member of the lab of Shannon Bailey, Ph.D., in the Division of Molecular and Cellular Pathology. Previous research has shown that the liver clock controls glycogen synthesis in a regular rhythm throughout the day. Emerging studies show that alcohol can disrupt the liver clock's timing, just as it disturbs the main circadian clock in the brain to disturb sleep and other behaviors.

Udoh's work connects these two observations. In mouse models, "we normally see a nice diurnal rhythm to glycogen content in the liver, which makes sense because metabolic needs vary throughout the day," Udoh says. But chronic alcohol consumption brings a significant change in that pattern, and a corresponding decrease in glycogen levels, Udoh found. She also demonstrated that alcohol disrupts signaling genes and proteins regulated by the liver clock that control glycogen metabolism.

Without sufficient glycogen, the liver may lack the energy to repair alcohol-generated damage, contributing to alcoholic liver disease. Ultimately, Udoh's research "highlights the molecular clock as a novel therapeutic target for alcoholic liver disease," says Bailey. (Learn more about Bailey’s own research into chronic alcohol consumption and the liver clock in this Mix podcast.)

Udoh's work was one of only six selected for presentation at the Research Society on Alcoholism meeting from hundreds of applications. Judges selected her for the Gordis award, which recognizes outstanding research among graduate students and postdoctoral fellows, based on her oral presentation and research poster session. One of the highlights of the event was discussing her work with Dr. Gordis himself, Udoh says. "It's a great honor."

Using 3D printers and movie modeling techniques, UAB researchers enhance workplace safety devices

Claudiu Lungu and a team from UAB's Department of Environmental Health Sciences have devised a high-tech, low-cost method for designing and fabricating new respirator prototypes to improve workplace safety.

If you work on an auto painting crew, stir vats of artificial butter at a popcorn factory or handle asbestos at a shipyard, you are one of the 5 million American workers legally required to wear respiratory protective equipment on the job.

But legal requirements and actual practice don't always match up. And even when workers wear their respirators, they may not be doing much good.

Studies show that hundreds of thousands of workers—from 15 to 20 percent, according to recent research—may be wearing ill-fitting respirators, not designed for a workforce that has rapidly changed over the past decades.

But a UAB research team has devised a high-tech, low-cost method for designing and fabricating new respirator prototypes to better match the variety of facial shapes in today's workplace. In addition to protecting industrial workers, the technology could aid members of the military as well. The findings are published online in the Journal of Occupational and Environmental Hygiene.