A sophisticated test of circulating tumor DNA in patients with gastrointestinal stromal tumors provided a more informative summary of the cancer's mutations—and yielded a larger number of secondary mutations that drive resistance to targeted therapies—than probing tissue samples from the same patients.

Thanks to a sophisticated technology that allows the detection and quantification of mutant DNA in a blood sample, researchers can track cancer-causing mutations associated with distinct responses to targeted drugs used to treat patients with gastrointestinal stromal tumors (GIST).

Data from a subanalysis of the phase III GRID study, designed to assess the efficacy of regorafenib (Stivarga; Bayer) in patients with GIST, indicates that the technology, called BEAMing (Beads, Emulsions, Amplification, and Magnetics), may offer physicians a real-time composite picture of the mutations across all tumors in any given patient, says George Demetri, MD, director of the Ludwig Center for Cancer Research at Dana-Farber Cancer Institute in Boston, MA, and the study's principal investigator.

Demetri presented his team's findings at the American Association for Cancer Research Annual Meeting 2013, held in Washington, DC, April 6–10.

Although sequencing tumor DNA can reveal GIST mutations in the cancer-related genes KIT and PDGFRA, “over time, tumors develop a clonal heterogeneity of resistance that makes diagnostics a challenge,” Demetri explains. Patients may eventually wind up with dozens of different mutations in different tumors, or even different mutations in different parts of any single tumor, so that detecting all of those mutations in a traditional biopsy would be nearly impossible, he says.

Because tumor cells are constantly dying as well as growing, the cells release fragments of DNA into the bloodstream; Demetri's team reasoned that analyzing mutations in the circulating DNA would provide “a more sensitive and accurate assessment of everything that's going on in the whole person,” he notes.

The researchers decided to analyze tumors from GIST patients who participated in the GRID study. First, they used conventional Sanger sequencing to analyze 102 archived tissue samples for mutations in KIT and PDGFRA, 2 genes that produce the cancer-driving proteins targeted by the tyrosine kinase inhibitors imatinib (Gleevec; Novartis), sunitinib (Sutent; Pfizer), and regorafenib.

Next, using the BEAMing technology, developed by Inostics (Hamburg, Germany) and customized with primers to amplify known mutations, they analyzed blood samples taken from 163 patients after the patients had developed resistance to imatinib and sunitinib.

The researchers detected KIT mutations in 58% of the blood samples compared with 66% of the tumor tissue samples. However, when focusing their analysis on secondary KIT mutations—those that drive resistance to targeted therapies such as imatinib and sunitinib—they found resistance mutations 4 times more often in the blood samples (48%) than in the tumor tissue samples (12%). Furthermore, nearly half of the blood samples that had secondary KIT mutations harbored multiple secondary mutations.

Compared with a placebo, regorafenib was clinically active in patients with secondary KIT mutations, says Demetri, showing a clear association between the presence of different cancer-driving gene mutations in circulating DNA and clinical outcomes.

“By using this technology,” Demetri says, “we hope to develop the most rational drug combinations and better tests to match patients with the most effective therapies going forward.”

Offered by Inostics of Hamburg, Germany, BEAMing performs single-molecule PCR on magnetic beads in water-in-oil emulsions (above). The core process transforms a population of DNA molecules into a population of beads, each coated with thousands of copies of an identical sequence, says the company, noting that BEAMing offers sensitivity and selectivity 100-fold higher than conventional PCR approaches. Using the technology to test circulating tumor DNA in patients with gastrointestinal stromal tumors provided a real-time composite picture of the cancer's mutations—and yielded a larger number of secondary mutations that drive resistance to targeted therapies—than probing tissue samples from the same patients.
View largeDownload slide

Offered by Inostics of Hamburg, Germany, BEAMing performs single-molecule PCR on magnetic beads in water-in-oil emulsions (above). The core process transforms a population of DNA molecules into a population of beads, each coated with thousands of copies of an identical sequence, says the company, noting that BEAMing offers sensitivity and selectivity 100-fold higher than conventional PCR approaches. Using the technology to test circulating tumor DNA in patients with gastrointestinal stromal tumors provided a real-time composite picture of the cancer's mutations—and yielded a larger number of secondary mutations that drive resistance to targeted therapies—than probing tissue samples from the same patients.

Offered by Inostics of Hamburg, Germany, BEAMing performs single-molecule PCR on magnetic beads in water-in-oil emulsions (above). The core process transforms a population of DNA molecules into a population of beads, each coated with thousands of copies of an identical sequence, says the company, noting that BEAMing offers sensitivity and selectivity 100-fold higher than conventional PCR approaches. Using the technology to test circulating tumor DNA in patients with gastrointestinal stromal tumors provided a real-time composite picture of the cancer's mutations—and yielded a larger number of secondary mutations that drive resistance to targeted therapies—than probing tissue samples from the same patients.
View largeDownload slide

Offered by Inostics of Hamburg, Germany, BEAMing performs single-molecule PCR on magnetic beads in water-in-oil emulsions (above). The core process transforms a population of DNA molecules into a population of beads, each coated with thousands of copies of an identical sequence, says the company, noting that BEAMing offers sensitivity and selectivity 100-fold higher than conventional PCR approaches. Using the technology to test circulating tumor DNA in patients with gastrointestinal stromal tumors provided a real-time composite picture of the cancer's mutations—and yielded a larger number of secondary mutations that drive resistance to targeted therapies—than probing tissue samples from the same patients.

Close modal

For more news on cancer research, visit Cancer Discovery online at http://CDnews.aacrjournals.org.

©2012 American Association for Cancer Research.
2012