An App for That

Developing a Practical Genomic Test for Radiation Exposure.

In the wake of September 11, 2001, the federal government committed billions of dollars to protect Americans from another attack – particularly one using weapons of mass destruction. The funding has gone into more than military operations; it has also driven scientific research aimed at developing new tests and treatments for use at future Ground Zeroes. Among the first researchers to enlist in this new offensive against potential terrorism were John Chute and his Duke colleagues, who have been developing a genome-based method to rapidly measure radiation exposure in the event of a nuclear event or “dirty bomb.”

“If a dirty bomb or an improvised nuclear device were to be used in a terrorist attack today, tens-to-hundreds of thousands of people could be exposed and an equal number petrified that they had been exposed,” said Chute, an associate professor of medicine and IGSP member. “We would need a way to triage those who had minimal or no exposure and needed no treatment, those who were lethally exposed and required comfort care, and those who had a level of exposure that could benefit from treatment. None of the current tests fits that bill.”

With funding from the Biomedical Advanced Research and Developmental Authority (BARDA), Chute and his collaborators are on course to correct that rather dismal state of affairs.

Basic Training

Chute seems a likely character to command such a mission, considering that he has spent much of his career in service to his country. He attended Georgetown University Medical School on a Navy scholarship, which he later paid back as a resident and attending physician at the National Naval Medical Center in Bethesda, Maryland. It was then that Chute began his own research at the Navy Medical Research Institute – an entity with a long history of research focused on the effects of radiologic or nuclear exposure on the troops. When he came to Duke in 2004, Chute was eager to expand his studies on the effects of radiation on the blood system, this time focusing on the genomic response to radiation exposure.

Scientists already knew that high doses of ionizing radiation could wreak havoc on the blood and immune systems, leaving the body vulnerable to infections and bleeding and increasing the risk of cancer. But these symptoms don’t show up until days to weeks after exposure, when it’s too late for treatments aimed at building back the body’s defenses. Methods available for measuring radiation injury – cytogenetics to look at damage to the cell’s 46 chromosomes or lymphocyte studies to count immune cells as they die off – simply take too much time in the event of a mass casualty.

“Changes in gene activity in the circulating blood can be an excellent sensor of exposure to injuries not visible to the human eye.”
—John Chute

So Chute joined forces at Duke with Nelson Chao, RadCCORE (Radiation Countermeasures Centers of Excellence) principal investigator, and the IGSP’s Holly Dressman and Joe Nevins to create a test based on gene chips to assess the body’s response to radiation at an even more fundamental level.

Dressman, Director of the IGSP’s DNA Microarray Core Facility, led an effort to subject mice to different doses of radiation and look for the impact of each dose on specific genes in the blood. That work showed that each radiation dose produced distinct gene patterns, which could be used to predict the degree of exposure. The researchers then repeated the same experiment in blood samples from human patients who had been treated with high doses of radiation, finding that a gene expression profile in human peripheral blood could be applied to predict the radiation status of people with high accuracy.

The researchers recognized that a number of variables – sex differences, genetic makeup, and time since exposure – might affect the precision of the test once they moved it out of the laboratory and into the real world. In a follow up study, Chute’s team showed that the test remained accurate, no matter what they threw at it.

Consistency Counts

The Duke team has now taken that laboratory test into the next stage of development with the aid of their BARDA funding, which could eventually reach more than $43 million. At the end of that time, Chute says they hope to have created a portable instrument that can screen thousands of samples – based on just a droplet of blood per person – in less than an hour.

To reach that goal, the Duke team essentially went back to the drawing board. They’ve teamed up with IGSP Computational Biologist Joe Lucas to identify those genes that consistently respond to radiation in the same way in mice, human blood samples and in patients exposed to radiation in the course of treatment for other medical conditions.

“We’ve got pretty compelling evidence now that our test should do what it is supposed to do,” Lucas says. He has been able to build predictors using the mouse and blood sample data that work in identifying radiation exposure in the human patients. The next step is to apply those predictors to non-human primates.

Lucas says that if the genes identified in mice and humans work in primates, there is every reason to think they would also work in an everyday group of healthy people after an accidental exposure, such as the one following the earthquake in Japan earlier this year, or an attack.

The Duke team will send that carefully selected list to a company called DxTerity Diagnostics, which has developed a proprietary technology that can essentially do the same work as a gene chip but in a more focused and less costly manner. The goal is to find those genes that translate well from one platform to the other.

“We want to use a drop of blood from a finger prick to look at a handful of genes, not thousands, and place people in bin A, B or C,” Dressman says. Chute says it now appears that as few as 15 genes might do the trick as far as a week out after exposure.

In August, BARDA recognized the project’s success with a grant renewal of $10.8 million. The Duke researchers are the only BARDA awardees to have reached this phase of the award and secured further funding. They plan to use the money over the coming year to develop the prototype assay and instrument with the end goal of government procurement in two years.

Chute’s team is also partnering with colleagues at the University of Arizona, an institution with a proven track record of turning homegrown academic center assays into practical diagnostics. For example, Frederic Zenhausern and his colleagues developed MiDAS, a desktop-printer sized instrument that the FBI now uses at crime scenes for rapid turnaround DNA fingerprinting. Chute envisions a similar instrument for his radiation assay.

Once a device is ready, Chute and his colleagues will help to verify its accuracy by gathering and testing as many as a thousand human samples from patients at Duke, as well as Dana Farber and Memorial Sloan Kettering, who have undergone radiation treatment in preparation for bone marrow transplant.

The Next Defense

If all goes as planned, that collaboration could lead to a critical first line of defense in the event of a nuclear attack, by creating a way to quickly and easily screen tens of thousands of people for radiation exposure. That would be a major coup, but RadCCORE Director Chao and others won’t be satisfied until they have a more comprehensive arsenal against the damaging effects of radiation.

“We are interested in studying the specific genes that came up in this genomic test,” Chao said. “We hope that by understanding the cellular pathways that are affected in response to radiation – such as oxidative stress or DNA repair – we may be able to figure out ways to block or enhance these pathways as therapies.”

Their team has identified a number of commonly used drugs that target the genes implicated in radiation response. Now they are screening those compounds to see which ones actually protect against radiation injury. Chute is quick to say that it is this glimpse into the biological underpinnings of the body’s response to radiation that excites him the most, especially given its treatment implications.

“At the end of the day, even if we are able to develop a wonderful test for radiation that can allow us to triage people based on their radiation exposure, we still have a substantial need to develop therapies for those people who need them most,” said Chute. “That is on our minds in all of the research studies that we are doing – how we can use the biology to identify and develop novel therapies to mitigate radiation injury – because that is the bottom line.”


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