Method could someday be used to assess treatment response
Cell-free DNA fragments shed into circulating blood may provide an important biomarker for monitoring the progression and treatment of glioblastoma (GBM), a highly aggressive brain cancer, according to a new study by researchers at TGen, part of City of Hope, and the Mayo Clinic.
Glioblastoma is difficult to monitor without repeated imaging, which doesn’t always capture the details of early tumor progression and variation. DNA shed by these tumors could provide a better glimpse of the cancer, but researchers aren’t sure how much the blood-brain barrier might limit the circulation of glioblastoma cell-free DNA, or if that DNA can be reliably distinguished from cell-free DNA shed by healthy brain cells.
The study, published in Journal of Neuro-Oncology, lays the groundwork for using cell-free DNA as a glioblastoma biomarker by analyzing cell cultures from two patient-derived glioblastoma cell lines.
“The origins of cell-free DNA have been relatively understudied. Understanding how the body releases it, what mechanisms drive that release, and how it fragments requires a tightly controlled environment that clinical research settings don’t typically offer,” said Sharvari Mankame, the lead author of the paper and a Ph.D. candidate in the Barthel lab at TGen.
Their analysis found differences in the genetic variants found in the cell-free DNA from the two glioblastoma lines. “GBM presents a very different tumor from patient to patient,” Mankame said. “That’s why it’s so hard to find one treatment that works for everyone. Each tumor is genetically unique.
Notably, the scientists found that most of the cell-free DNA shed by the cell cultures came from viable cells, not dead or dying ones, a result that ran counter to what they’d expected. That pattern changed, however, once the scientists treated the cell cultures with the glioblastoma drug temozolomide.
Temozolomide increased levels of detectable cell-free DNA and shifted its source from viable cells to dead cells. The treatment also increased fragmentation and reduced the amount of genetic diversity found in the cell-free DNA. The researchers confirmed the same trends in cell-free DNA retrieved from mice with glioblastoma tumors.
“This kind of cell-free DNA signal is how we might someday longitudinally assess or differentiate between a growing tumor or a shrinking tumor,” said Floris Barthel, M.D., Ph.D., an assistant professor in TGen’s Bioinnovation and Genome Sciences Division and the paper’s senior author.
The research team also looked at glioblastoma cells cultured with brain cells called astrocytes. They found that they could distinguish between cell-free DNA derived from both cell types. In these co-cultures, the source of cell-free DNA changed over time, as the glioblastoma cells outcompeted and killed the astrocytes, leading to more cell-free DNA from the dead or dying astrocytes.
“We were able to isolate tumor signal really well from the normal signal, which is exactly what we do in clinical settings,” Barthel said.
It took two years to get the cells to grow reliably in the lab, and each experiment had to be repeated three times to get results that could be trusted statistically. The goal was to understand how cell-free DNA might work as a biomarker. According to Mankame, the next step is to track cell-free DNA over a longer period in patients, to see how it changes after weeks or months of treatment.
TGen researchers on the study also included Distinguished Professor Nhan L. Tran, Ph.D., director of the Immunology and Microbiome Division, and Professor Michael E. Berens, Ph.D., head of the Glioma Research Lab.
A 2022 American Brain Tumor Association Discovery Award supported this research.
Becky Ham, TGen
Posted on Tuesday, October 06, 2026