Tracking Resistance to Cancer Therapies Without Tumor Access

Clinicians would like to be able to monitor whether a cancer patient’s tumor has acquired a resistance mutation as a result of targeted therapy. Knowing early if resistance has developed would allow patients to switch therapies and to curb tumor growth. But taking repeated tumor samples is problematic for many reasons. Biopsies are invasive and some tumors are inaccessible. Another issue is that tumors are mosaics of many different types of cells that are constantly evolving—since biopsies take time in the clinic and only sample a small part of a tumor, they may also not be representative of what is going on with the biology of the entire tumor mass.

To circumvent the issue, researchers are developing what are called ‘liquid biopsies’ to track the development of resistance by analyzing the cell-free tumor DNA that circulates in the blood stream. In a proof of principle study, researchers from the University of Cambridge and the Cancer Research UK Cambridge Institute, in the UK have been able to track the genetic evolution of six metastatic breast, ovarian, and lung cancer patients in response to therapy. The study was published in the journal Nature; (abstract).

In a different study, the same set of researchers also demonstrated that this liquid biopsy could be more effective and sensitive than current biomarkers approved by the U.S. Food and Drug Administration (FDA) for monitoring tumor burden and progression of metastatic breast cancer patients (abstract). Sarah-Jane Dawson, PhD, and colleagues found that 97% of the 30 women in the study had detectable circulating tumor DNA (ctDNA) compared to 78% of women who had detectable levels of the cancer antigen (CA) 15-3 biomarker and 87% of women who had circulating tumor cells (CTCs) detected. ctDNA was also found to have a better predictive value compared to CA 15-3. While both CTCs and ctDNA levels correlated with prognosis, ctDNA had a more dynamic range that paralleled the changes in tumor burden.

The technique is also being developed by other research groups around the world, including groups at Johns Hopkins University in Baltimore, Maryland and the Institute for Cancer Research and Treatment in Turin, Italy. Thus far, the ctDNA approach appears more promising than analyzing the CTCs that are also found in the blood of cancer patients. Compared to CTCs, ctDNA is more easily accessible and is easier to process.

In the metastatic breast cancer study, Dawson and colleagues from the Cancer Research UK Cambridge Institute, used both targeted sequencing to identify mutations in two genes, PI3K and TP53, as well as whole genome sequencing of tumor samples. The researchers then took serial plasma samples to quantify ctDNA and track the mutations identified from tumor samples.

In the study published in Nature, the researchers took multiple samples of patients’ plasma over the course of 1 to 2 years, performing whole-exome sequencing to track tumor mutations in several genes, including PIK3CA and EGFR. Muhammed Murtaza, also from the Cancer Research UK Cambridge Institute, and colleagues, followed changes in the abundance of DNA mutation fragments in plasma, as patients went through courses of targeted treatments. For example, an acquired resistance mutation to the oral EGFR inhibitor gefitinib was identified in a non-small cell lung cancer patient who was being treated with the drug. The emergence of the resistance mutation was at the same time that the patient began to progress while on the treatment.

Researchers hope that detecting these resistance mutations in ctDNA can be a way to understand the evolving genetics of a patient’s tumor quickly and change or alter treatment.

For now, monitoring of a specific gene alteration of a tumor through ctDNA requires an initial identification of that mutation. But, as whole-genome sequencing becomes more affordable and accessible, targeted ctDNA sequencing will become more prevalent, allowing for nontargeted approaches. These studies and others that have been recently published show that the DNA fragments circulating in the blood of a cancer patient are indeed representative of the patient’s tumor genome.

In an editorial accompanying the metastatic breast cancer study, C. Kent Osborne, MD, of the Baylor College of Medicine in Houston, Texas, and Marc Lippman, MD, of the Leonard M. Miller School of Medicine at the University of Miami in Florida, state that the study shows ctDNA to be a sensitive biomarker of patient tumor burden and can be used cost-effectively to improve care of metastatic cancer patients.