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Mt. Sinai Studying CTCs, ctDNA in Context of Triple Negative Breast Cancer


NEW YORK (GenomeWeb) – Over the last several years, the liquid biopsy field has been booming. Researchers and molecular diagnostic developers have been working on noninvasive means to genomically profile cancer patients' tumors by analyzing either the cancer cells that circulate in their blood or the fragmented pieces of circulating cell-free tumor DNA as a proxy for the patient's actual tumor.

Analyzing CTCs and ctDNA each have their challenges: CTCs are rare, but if they can be singled out and the DNA extracted, it is typically high quality and amenable to analysis, while ctDNA is highly degraded and fragmented. Researchers have debated the merits and drawbacks of each, trying to figure out how to develop the most sensitive and accurate liquid biopsy test.

Increasingly, however, researchers see value in analyzing both, and now a team from the Icahn School of Medicine at Mount Sinai plans to evaluate both the genomic profiles of ctDNA and CTCs as well as phenotypic features of CTCs in patients with triple negative breast cancer to study the relationships between the two and how they correlate with disease.

Michael Donovan, an anatomic pathologist at Mt. Sinai, discussed the trial in a presentation at the Cambridge Healthtech Institute Molecular Medicine Tri-Conference in San Francisco and in a follow-up interview with GenomeWeb.

The group plans to enroll 53 triple negative breast cancer patients who are being treated at Mt. Sinai and will analyze samples from patients at diagnosis, after treatment, and at six-month intervals for 18 months. They will use Cynvenio's LiquidBiopsy microfluidic system to isolate CTCs, ctDNA, and germline DNA and will analyze the genomic content using Thermo Fisher's AmpliSeq Hotspot and Oncomine panels on the Ion Torrent PGM and S5, respectively, as well as morphology and other phenotypic features of the CTCs.

The trial is slated to start in about four weeks and will run for between 18 months and two years.

Already, the team has completed a 15-patient pilot study. Donovan presented a couple of case examples in a presentation at the Tri-Conference meeting. In one case Donovan described identifying a PIK3CA mutation in the patient at diagnosis, which was eliminated following chemotherapy treatment.

The correlative association trial is purely research-based, Donovan said, so results of the CTC and ctDNA genomic analyses will not be returned to patients or be used to make treatment decisions. Rather, the trial is designed to figure out how CTCs and ctDNA track with disease progression and response to standard of care treatment.

"We'll [aim to] understand not only the quantitative assessment of CTCs, but more importantly, assess their morphologic attributes and combine this information with the DNA profile of both the CTC population and the cell-free DNA," Donovan said.

Donovan added that the group would study morphologic attributes of CTCs such as how the cells clusters, their cytoplasmic granularity, and physical characteristics such as the size and shape of cells. "There are some theories that smaller CTCs, for instance, are potentially a different population," he said. They tend to be more mobile and cluster together, he added. In addition, he said there is some emerging evidence that these smaller, more mobile cells may play a role in the dissemination of cancer throughout the body.

Because the trial will enroll patients at any stage of their disease — from stage I to IV — researchers will also be able to study whether there are differences in the type of CTCs depending on the stage of disease. For instance, patients with metastases may have different CTCs than patients with stage I disease. "There may be an increase in the cancer stem cell population in metastases," Donovan said, and such cells may have a "unique genomic profile," although that has yet to be proven.

Analyzing the genomics of both ctDNA and the CTCs will enable the team to try and correlate physical features with the genomics. Donovan said one goal would be to look at the concordance between ctDNA and CTC genomic profiles. Understanding when ctDNA and CTCs are concordant and discordant and what factors are associated with each will be "informative to understanding the role" that each plays and in understanding what each is reflecting. It will also be technically challenging, particularly in the case of low-frequency variants, to discern whether discordant results are true discrepancies or sequencing errors.

Donovan said that he expects there to be real differences between the genomic profiles of CTCs and ctDNA in some cases. For one, the mechanisms by which they arise in the blood are completely different, he said. CTCs are for the most part living cells, he said, while ctDNA is shed into the blood from dying cells — from either apoptotic or necrotic processes. There could even be different genomic profiles among different populations of CTCs. For instance, CTCs that are cancer stem cells could carry a different set of mutations than other CTCs.

The Cynvenio system also allows for the collection of germline DNA, Donovan said, so the researchers can compare genomic profiles from all three sample types.

Donovan said that aside from the trial focused on triple negative breast cancer, the Mt. Sinai team has been using the Cynvenio system to process samples from patients with all types of breast cancer who consent to research.

Separately, Cynvenio is also conducting its own trial using its LiquidBiopsy platform to analyze CTCs and ctDNA from triple negative breast cancer patients. It launched a pilot surveillance study in collaboration with South Korea's ATGen Global last year, and is using both its ClearID targeted genomic test and ATGen's NK Vue test, which measures activity of natural killer cells — a component of the immune system that attacks tumor cells.