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Urine Biopsies Detect Early Mutations in Patients with Advanced Cancers

August 2015 Vol 8, Special Issue: Payers' Perspectives in Oncology

An assay that measures circulating tumor (ct) DNA in the urine can detect mutations in patients with a variety of advanced cancers, according to a study presented at ASCO 2015.

Coexistence of BRAF and KRAS Mutations

“We found some emerging data that even though BRAF and KRAS were deemed to be mutually exclusive, in some patients with BRAF mutations, you can actually find low frequency clones of KRAS in the cell-free DNA, which might potentially reflect tumor heterogeneity and the resistant clones which might ultimately emerge because of selection pressure,” said Filip Janku, MD, PhD, of the Department of Investigational Cancer Therapeutics, M.D. Anderson Cancer Center, Houston, TX.

Of 34 patients with the BRAF V600E mutation in the tumor, 32 (94%) also had detectable BRAF 600E mutation in their urine. In 25 of 34 (74%) patients analyzed longitudinally, changes in cell-free DNA BRAF V600E copies correlated with percentage changes in target lesions on imaging studies. “The number of patients with KRAS mutations goes up as well as the number of detected KRAS mutations,” Dr Janku said.

Urinary cell-free DNA was able to detect acquisition of KRAS G12/13 in patients treated with BRAF- or MEK-targeted therapy. Some patients without a KRAS mutation that was detected before treatment had KRAS mutations emerge during treatment, said Dr Janku.

Of the 31 patients who were tested for urinary KRAS G12/13 mutations, 25 (81%) had low-frequency KRAS G12/13 mutations on at least 1 test, and these were not detected in tumor samples by standard tissue technologies. In addition, 11 patients had detectable urinary KRAS mutations before treatment and 19 patients had these detected during treatment.

“The next step, once we figure out how we can monitor the clonal evolution, is to test acting on the information in clinical trials,” said Dr Janku.

EGFR Resistance Mutations

In a second study, early acquisition of epidermal growth factor receptor (EGFR) resistance mutations in patients with metastatic lung adenocarcinoma was found by measuring ctDNA in the urine.

Acquired resistance to EGFR tyrosine kinase inhibitors (TKIs) develops in most patients by 12 months. The secondary T790M mutation occurs in about 60% of patients with acquired resistance to EGFR TKIs, according to Hatim Husain, MD, Assistant Professor of Medicine, Division of Hematology-Oncology, Moores Cancer Center, University of California, San Diego, and colleagues.

An EGFR resistance T790M mutation was detected in urinary ctDNA months before progression with anti-­EGFR TKIs. The urine-based testing system extracts ctDNA from urine samples and uses polymerase chain reaction to amplify small DNA fragments while enriching for mutant alleles. The urine-based biopsy provides a noninvasive alternative to tissue biopsy in relapsed patients to detect T790M.

Among 14 metastatic lung cancer patients with tissue-confirmed T790M, urine T790M was detected in all 14.

Dr Husain’s group also found that T790M could be identified before radiographic progression of disease. The 24 patients who received erlotinib were monitored for acquisition of the T790M mutation through the use of urinary ctDNA, which was collected every 3 to 6 weeks. “T790M mutation was detected as early as 3 months prior to radiological progression,” the investigators found.

Future studies should characterize the therapeutic implications of earlier intervention with second-line therapy in patients who have early acquisition detected through the use of the urine assay, Dr Husain advised.

Last modified: August 30, 2021