Priming Agents Maximize ctDNA Availability for Liquid Biopsies

CAMBRIDGE, MA — Tumors constantly shed DNA from dying cells, which briefly circulates in the patient’s bloodstream before it is quickly broken down. Many companies have created blood tests that can pick out this tumor DNA, potentially helping clinicians diagnose or monitor cancer or choose a treatment.

The amount of tumor DNA circulating at any given time, however, is extremely small, so it has been challenging to develop tests sensitive enough to pick up that tiny signal. A team of researchers from MIT and the Broad Institute of MIT and Harvard has come up with a way to significantly boost that signal, by temporarily slowing the clearance of tumor DNA circulating in the bloodstream.

The researchers developed two different types of injectable molecules that they call “priming agents,” which can transiently interfere with the body’s ability to remove circulating tumor DNA (ctDNA) from the bloodstream. This approach, published recently in Science, could enable not only earlier diagnosis of cancer but also more sensitive detection of tumor mutations that could be used to guide treatment. It could also help improve the detection of cancer recurrence.

“You can give one of these agents an hour before the blood draw, and it makes things visible that previously wouldn’t have been. The implication is that we should be able to give everybody who’s doing liquid biopsies, for any purpose, more molecules to work with,” says Sangeeta Bhatia, MD, PhD, the John and Dorothy Wilson professor of health sciences and technology and of electrical engineering and computer science at MIT, and a member of MIT’s Koch Institute for Integrative Cancer Research and the Institute for Medical Engineering and Science.

Better biopsies

Liquid biopsies are now used in many cancer patients to identify mutations that could help guide treatment. With greater sensitivity, however, these tests could become useful for far more patients. Most efforts to improve the sensitivity of liquid biopsies have focused on developing new sequencing technologies to use after the blood is drawn. While brainstorming ways to make liquid biopsies more informative, Bhatia, the co-authors, and their trainees came up with the idea of trying to increase the amount of DNA in a patient’s bloodstream before the sample is taken.

“A tumor is always creating new cell-free DNA (cfDNA), and that’s the signal that we’re attempting to detect in the blood draw. Existing liquid biopsy technologies, however, are limited by the amount of material you collect in the tube of blood,” J. Christopher Love, PhD, Raymond A. and Helen E. St. Laurent professor of chemical engineering, MIT, said. “Where this work intercedes is thinking about how to inject something beforehand that would help boost or enhance the amount of signal that is available to collect in the same small sample.”

The body uses two primary strategies to remove ctDNA from the bloodstream. Enzymes called DNases circulate in the blood and break down DNA that they encounter, while immune cells known as macrophages take up cfDNA as blood is filtered through the liver.

The researchers decided to target each of these processes separately. To prevent DNases from breaking down DNA, they designed a monoclonal antibody that binds to ctDNA and protects it from the enzymes. “Antibodies are well-established biopharmaceutical modalities, and they’re safe in a number of different disease contexts, including cancer and autoimmune treatments,” Love says. “The idea was, could we use this kind of antibody to help shield the DNA temporarily from degradation by the nucleases that are in circulation? And by doing so, we shift the balance to where the tumor is generating DNA slightly faster than is being degraded, increasing the concentration in a blood draw.”

The other priming agent they developed is a nanoparticle designed to block macrophages from taking up cfDNA. These cells have a well-known tendency to eat up synthetic nanoparticles. “DNA is a biological nanoparticle, and it made sense that immune cells in the liver were probably taking this up just like they do synthetic nanoparticles. And if that were the case, which it turned out to be, then we could use a safe dummy nanoparticle to distract those immune cells and leave the circulating DNA alone so that it could be at a higher concentration,” Bhatia says.

Earlier tumor detection

Early detection of cancer is a promising application for these priming agents. The researchers found that when animal models were given the nanoparticle priming agent before blood was drawn, it allowed them to detect circulating tumor DNA in blood of 75 percent of the models with low cancer burden, while none were detectable without this boost.

After either of the priming agents is injected, it takes an hour or two for the DNA levels to increase in the bloodstream, and then they return to normal within about 24 hours. “The ability to get peak activity of these agents within a couple of hours, followed by their rapid clearance, means that someone could go into a doctor’s office, receive an agent like this, and then give their blood for the test itself, all within one visit,” Love says. “This feature bodes well for the potential to translate this concept into clinical use.”

“A tube of blood is a much more accessible diagnostic than colonoscopy screening or even mammography,” Bhatia says. “Ultimately, if these tools really are predictive, then we should be able to get many more patients into the system who could benefit from cancer interception or better therapy.”

- This press release was originally published on the Massachusetts Institute of Technology website