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In a new study published in the journal Clinical Cancer Research, researchers from the University of Pennsylvania are the first to demonstrate that glioblastoma (GBM) patients with a higher concentration of cell-free DNA (cfDNA) have a shorter progression-free survival after they are diagnosed compared to patients with less cfDNA, and that cfDNA concentrations increase in patients at the time of, or just before, their disease progresses.



What is cfDNA?



Erica Carpenter, Ph.D., director of the Liquid Biopsy Laboratory and a research professor of Medicine at Penn, told Technology Networks: "Cell-free DNA is the free DNA that is found circulating in blood that has been released by dying cells. It is typically fragmented into small pieces. Cell-free DNA is shed by most types of cells in the body and thus can be found in the blood of all individuals, even when healthy."



A blood test that measures the level of cfDNA in the bloodstream is known as a liquid biopsy. These types of blood tests are being increasingly used in diagnostic medicine, particularly in cancer. Carpenter says: "Since the tumor cells of cancer patients also shed cell-free DNA, a cancer patient will often have a portion of their cell-free DNA that originated in the tumor. This cell-free tumor DNA provides us with a non-invasively accessible “liquid biopsy” that molecularly represents the genetic signature of the tumor."



"Doctors have begun using liquid biopsies more frequently to monitor certain cancers - particularly lung cancer - in recent years as research has shown their effectiveness in other disease sites. But until now, there has been little focus on the clinical utility of liquid biopsy in brain tumors," she adds.



Difficulties in tackling an aggressive form of cancer



The research study cohort included 42 patients that had received a new diagnosis of GBM, a particularly aggressive form of brain cancer. The five-year survival rate for GBM patients is between five and 10 percent. A challenge for physicians treating these patients is that monitoring GBM via imaging can prove inaccurate, and the tumors are often heterogenous, meaning different sections of the tumor contain different genetic mutations. Consequently, treatments targeting one particular area of the tumor may not be effective against other parts of the tumor.



Of further concern is that obtaining a tissue sample for analysis in GBM patients requires a repeat brain surgery, making it difficult to track the progression of the cancer without extremely invasive procedures.



The study's lead author Stephen J. Bagley, M.D., an assistant professor of Hematology-Oncology in Penn's Perelman School of Medicine, says: "There are many challenges associated with our current diagnostic approaches to brain tumors. Repeatedly obtaining tumor tissue from the brain is highly invasive and risky, so we are currently limited in our ability to monitor the genetics of brain tumors during the course of treatment. We also have a hard time predicting which patients with newly diagnosed brain tumors, such as glioblastoma, will do well with standard of care treatment and which patients will do poorly. "



He continues, "Lastly, and perhaps most problematic, our currently available imaging scans of the brain are not as accurate as we'd like for assessing response to treatment. Damage from brain radiation and tumor growth can look very similar on an MRI, for example. The ability to serially monitor cell-free DNA in the blood, or in other fluids such as cerebrospinal fluid, may ultimately be able to help address these problems in patients with brain tumors."



Tumor biopsy vs liquid biopsy



In this study, the 42 GBM patients had a number of blood tests taken, at diagnosis, before tumor removal, and at regular intervals throughout the course of their chemotherapy treatment.



Carpenter says: "When a patient provides a blood sample, plasma – also known as the liquid, acellular fraction of whole blood – is obtained by centrifugation. Cell-free DNA can then be extracted from the plasma and used as an input for downstream molecular analysis. In our study, the analysis was achieved through a process known as next-generation sequencing, in which a panel of genes was analyzed for mutations across all the coding regions of each gene."



28 patients were found to have a lower concentration of cfDNA pre-surgery. This was defined as cfDNA that was below the average calculated for the entire cohort. These patients were found to have almost double the progression free survival (9.5 months) when compared to the 14 patients that had higher concentrations of cfDNA (median 4.9 months).



The researchers also compared the genetic sequencing of solid tissue biopsies in GBM with the liquid biopsy results. They found that, whilst both biopsies detected genetic mutations in >50% of patients, none of the mutations overlapped. This suggests that liquid biopsies may be able to offer complimentary information to traditional tissue biopsies. "If liquid biopsy can give us a more comprehensive view of the molecular profile of the tumor, we can potentially pick more effective combinations for each patient," Bagley said.



Towards practice-changing research



The next steps for the scientists are to confirm their initial results from this small sample pilot study in a larger cohort of patients with GBM. They emphasize that the current results are hypothesis-generating rather than practice changing.



Bagley says: "We aim to confirm our initial results from this small pilot study in a larger cohort of patients with glioblastoma. In addition, we plan to more comprehensively assess the genetics of these tumors by sequencing the DNA of multiple pieces of the same tumor in an individual patient, and then comparing those results to what we see from sequencing the tumor DNA in the blood. Since these glioblastoma tumors are notoriously heterogenous, meaning that the tumor genetics can vary in different parts of the same tumor, we hypothesize that adding liquid biopsy to standard tumor sequencing may generate a more complete picture of the tumor's genetics."



Reference: Bagley et al. 2019. Clinical utility of plasma cell-free DNA in adult patients with newly diagnosed glioblastoma - a pilot prospective study. Clinical Cancer Research. DOI: 10.1158/1078-0432.CCR-19-2533.



Dr Erica Carpenter and Dr Stephen Bagley were speaking with Molly Campbell, Science Writer, Technology Networks.