Using radiation to boost circulating DNA for ‘liquid biopsies’ of cancer

Testing for tumor DNA in blood is easier and safer than taking a biopsy of tumor tissue. The problem is, early-stage tumors may not shed enough DNA to find in a blood draw.

Researchers at OHSU are working on a way to use radiation to increase the amount of tumor DNA in blood. They’ve shown that patients with suspected lung tumors show a sharp increase in circulating tumor DNA after treatment with stereotactic body radiation therapy, or SBRT.

Kathryn Baker, Ph.D.

“We are seeing a nice peak, a 25-fold increase on average,” said project co-leader Kathryn Baker, Ph.D., a postdoctoral scholar in CEDAR, the Knight Cancer Institute’s Cancer Early Detection Advanced Research Center. “It’s a very strong signal, but the timing of that peak is variable between patients.”

The researchers call it radiation-assisted amplification sequencing, or Ramp-Seq. “It’s a novel use of radiation,” said project co-leader Nima Nabavizadeh, M.D., an assistant professor of radiation medicine in the OHSU School of Medicine. He began developing the idea with Christopher Boniface, a doctoral student and manager in the laboratory of Paul Spellman, Ph.D., co-director of CEDAR.

A happenstance observation prompted the idea for Ramp-Seq: A patient had received palliative radiation to the spine while having blood samples tested for circulating tumor DNA. Boniface said they saw a 40-fold increase in tumor DNA over the course of palliative radiation.

Christopher Boniface

“Levels went from undetectable to abundant,” Nabavizadeh said, as cells killed by radiation released their DNA into the bloodstream. The researchers realized that this effect could prove useful, particularly for patients with suspicious lung nodules, often detected incidentally or by screening with low-dose computed tomography. When the clinical suspicion for lung cancer is high, but it’s unsafe to do a needle biopsy or surgically remove tissue, it is standard to treat such patients with radiation.

“For many high-risk patients, empiric treatment with SBRT is safer than putting the patient through an invasive biopsy,” Nabavizadeh said. The tradeoff is that a few patients will have lung nodules that are not cancerous and receive unnecessary full ablative-dose radiation treatment.

Nima Nabavizadeh, M.D.

A sensitive and specific blood testing blood for tumor DNA could reveal which patients have cancer. “It would help us figure out which patients do and don’t need a full definitive course of radiation therapy in the early screening population,” Nabavizadeh said. “For patients post-treatment and in surveillance, we very frequently see suspicious lesions on follow-up imaging where a biopsy would be very challenging. This approach could help decide whether or not it’s time to restart chemo, or put them through surgery or radiation.”

Because it is standard for high-risk patients with lung nodules to be treated with SBRT, it made sense to enlist them for a pilot study of Ramp-Seq. To date, the research team has collected blood from about 30 patients. Baker said they take a baseline blood draw, and further samples at intervals while patients undergo SBRT and after treatment ends. They sequence the cell-free DNA in blood samples and look for a set of mutations commonly found in lung cancer cells.

Bonifice presented data on the first eight cases at the American Association for Cancer Research Advances in Liquid Biopsy Meeting in January. He said the 25-fold average boost in tumor DNA wasn’t uniform in all eight patients, but each showed a measurable peak. That’s significant because circulating tumor DNA is undetectable in about half of people with confirmed stage 1 lung cancers.

In an interview with GenomeWeb, Boniface said that although the data is preliminary, it suggests that Ramp-seq may be feasible for use in cancer early detection and mutation profiling of masses that are difficult to biopsy or characterize.

Much work remains, including establishing that the detected DNA reliably indicates cancer. For the next step, the researchers are planning a protocol to give a single test dose of radiation to patients scheduled for surgery to remove a suspected lung tumor. They will then be able to sequence tumor DNA directly and compare it to sequences of cell-free DNA in blood.

They also need to define the optimal timepoints for collecting blood after the test-dose of radiation treatment. The variable timing of the surge in circulating DNA poses a challenge. In some cases, the increase occurs after 3 or 4 days, in others occurs it’s after 24 hours, in still others it’s not until 15 days after radiation.

“We would like to see an average time window in which to take blood, analyze the cell-free DNA and make a call,” Baker said. “We don’t know yet if it’s going to translate into something that’s easy to standardize.” Developing a test that is practical for clinical use has been part of Baker’s thinking form the beginning.

If Ramp-Seq proves effective, it could be implemented with existing technology. SBRT and gene sequencing are already widely available. And although the pilot is in lung cancer, if Ramp-Seq works, the researchers think it could be applied for other tumor types that are difficult or impossible to biopsy.

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