DNA in Urine Shows Promise as a Liquid Biopsy for Cancers and Rare Diseases

Urinary cell-free DNA analysis had near-100% accuracy for detectingBRAFmutations associated with histiocytic disease, according to a small clinical study¹reported at the 2014 ASCO Annual Meeting in Chicago.

Analysis of cell-free DNA in urine and plasma specimens from 22 patients with Erdheim-Chester disease or Langerhans cell histiocytosis showed the DNA test correctly identified all 10 patients with biopsy-confirmed mutations and ruled out mutations in all six patients with biopsy-confirmed wild-type tumors. Additionally, four patients had failed biopsy tests, and two patients did not have biopsy results.

The high level of performance by the cell-free DNA analysis has persisted in ongoing testing that increased the total number of patients to 26, said Omar Abdel-Wahab, MD, a myeloid diseases specialist at Memorial Sloan Kettering Cancer Center in New York. The test also has wide-ranging potential for identifying other types ofBRAF-mutant disease.

Eli L. Diamond, MD, Discusses the Trial

Diamond is a neurologist at Memorial Sloan Kettering Cancer Center.

“The same technology could be applied to anyBRAF-mutant disease,” said Abdel-Wahab. “In fact, this is ongoing currently in a study²at MD Anderson Cancer Center by Filip Janku, where he is measuringBRAF-mutant allele burden in urine and plasma of many cancer patients of various types.”

The technology can be adapted to identify other types of oncogenic mutations, Abdel-Wahab continued. Work has already begun on development of cell-free DNA tests for detection ofEGFR,PIK3CA,KRASandNRASmutations. Urine-based cell-free DNA testing forBRAF V600EandKRASmutations is already commercially available.

“The same technology can be used to detect virtually any point mutations,” he said. “Several groups are working on sequencing large numbers of genes in cell-free DNA as well.”

Though a rare clinical entity, histiocytic disease provided a good candidate for evaluating the cell-free DNA assay because of the disease’s high frequency of theBRAF 600Emutations and high response to treatment with RAF inhibition.

Omar Abdel-Wahab, MD

Abdel-Wahab and colleagues evaluated the DNA test in patients with knownBRAFmutation status, using droplet digital polymerase chain reaction (PCR) technology. In addition to patients with interpretable biopsy results, two patients without biopsy data were evaluated by urinary cell-free DNA assay, and both tested positive for theBRAFmutation. Analysis of cell-free DNA from plasma of the patients with histiocytic disease did not identify additional patients withBRAF-mutant disease that had not been identified by analysis of urinary cell-free DNA.

“Detection of actionableBRAFmutations by droplet digital PCR in cell-free DNA is feasible and was completely concordant with CLIA-certified tumor mutation testing,” Abdel-Wahab and colleagues concluded in a poster presentation. “Moreover, the ability to detectBRAFmutations in the urine of patients with repeated tumor tissue testing failure is potentially practice changing and demonstrates the clinical utility of cell-free DNA technologies.”

The study is notable as one of the few reported thus far to incorporate mutation analysis of tissue, urine, and blood, said invited discussant Ben Ho Park, MD, PhD, of Johns Hopkins Medicine in Baltimore, Maryland.

“The results are pretty exciting because there were even some cases where tissue could not adequately be queried for—meaning that the quality of the tissue wasn’t there so that they could reliably do mutation analysis,” said Park. “You can now take urine and blood and use that almost as a surrogate, for a liquid biopsy purpose, to see whether or not a patient is harboring aV600Emutation.”

A published abstract from the ASCO meeting provided evidence that longitudinal analysis of urinary cell-free DNA might have utility in monitoring patients withBRAF-mutant tumors for treatment response. Submitted by investigators headed by Janku, an assistant professor of investigational cancer therapeutics at MD Anderson Cancer Center, the study involved 17 patients with advanced, biopsy-provenBRAF-mutant cancers, including melanoma, non-small cell lung cancer, and colorectal cancer.

The patients underwent serial analyses of urinary cell-free DNA, which demonstrated statistically significant correlation inBRAF V600Emutation load and imaging-confirmed treatment response to targeted therapy. Specifically, patients with a decrease inBRAF V600Eload had a significantly longer median time to treatment failure (259 days vs 61 days,P= .002).

KRASmutation analysis for the 7 most common mutations from urine is currently available through Trovagene’s Clinical Laboratory Improvement Amendments (CLIA) lab, which uses next-generation sequencing technology. The company is currently working on anEGFRmutation analysis for lung cancer, including theT790Mmutation, which is a marker of resistance to erlotinib.

Clinical Pearls

• Urinary cell-free DNA analysis had near-100% accuracy for detectingBRAFmutations associated with Erdheim-Chester disease or Langerhans cell histiocytosis.
• An ongoing study is measuringBRAF-mutant allele burden in urine and plasma of many cancer patients of various types.
• Work has begun on development of cell-free DNA tests forKRASandNRASmutations.
• Analysis of cell-free DNA from plasma of the patients with histiocytic disease did not identify additional patients withBRAF-mutant disease that had not been identified by analysis of urinary cell-free DNA.
• The study is one of the few reported to incorporate mutation analysis of tissue, urine, and blood and provided evidence that longitudinal analysis of urinary cell-free DNA might have use in monitoring patients withBRAF-mutant tumors for treatment response.
• KRASmutation analysis for the 7 most common mutations from urine is currently available through Trovagene’s CLIA lab. NRAS and PIK3CA are among the future markers also being developed. Studies in KRAS are already open and accruing.

NRAS and PIK3CA are among the future markers also being developed. Studies in KRAS are already open and accruing. The University of Southern California is the study site for the colorectal study, and US Oncology/Scottsdale Healthcare/University of California, San Francisco are the sites for the pancreatic cancer study. A melanoma BRAF study collaboration was just announced with the Dana-Farber Cancer Institute as well, with Jason Luke as the principal investigator.

References

1. Abdel-Wahab OI, Diamond MP, Holley VR, et al. Detection of BRAF mutations in urine and plasma cell-free DNA: application to the diagnosis and management of histiocytic disorder patients. Poster presented at: 50th Annual Meeting of the American Society of Clinical Oncologists; May 30-June 2, 2014, Chicago, IL. Abstract 11012.
2. Janku F, Vibat CR, Falchook GS, et al. Longitudinal monitoring of BRAF V600E mutation in urinary cell-free DNA of patients with metastatic cancers.J Clin Oncol. 2014;32(suppl). Abstract e22175. http://meetinglibrary.asco.org/content/130132-144. Accessed June 18, 2014.