New ‘Liquid Biopsy’ Helps to Improve Breast Cancer Diagnostics and Avoid Unnecessary Surgeries

A new type of blood test for breast cancer may help avoid thousands of unnecessary surgeries and, at the same time, precisely monitor disease progression, according to study results published in the journal Science Translational Medicine.*

Tumor DNA shed into a patient’s circulation has shown great potential as a noninvasive method of detecting the presence of a tumor and analyzing its DNA for targetable mutations. But in patients who have already undergone initial chemotherapy treatment it can be difficult to detect small amounts of tumor DNA in the blood.

Muhammed Murtaza, MBBS, Ph.D., Assistant Professor and Co-Director of TGen’s Center for Noninvasive Diagnostics. Photo Courtesy: TGen, Phoenix, AZ.

To address this problem, a team of scientists led by Translational Genomics Research Institute (TGen) in Phoenix, Arizona and Mayo Clinic in Arizona, developed a customized method for each patient. The test can then be used to monitor the patient over time for and allow early detection of tumor recurrence.

The study results demonstrate that this test, called TARgeted DIgital Sequencing or TARDIS, is up to 100 times more sensitive than other blood-based cancer monitoring tools using clinically relevant blood volumes. This shows that personalized ctDNA tracking could enable individualized clinical management of patients with cancer treated with curative intent.

International Collaboration
TGen is an affiliate of City of Hope, which along with The Cancer Research UK Cambridge Institute at Cambridge University and the Biodesign Institute at Arizona State University (ASU) also contributed to this study.

This study was performed in collaboration with Carlos Caldas, MD, Professor of Cancer Medicine at the University of Cambridge and Director of the Breast Cancer Programme at the Cancer Research UK Cambridge Cancer Centre.

Preciscion
TARDIS is a “liquid biopsy” that specifically identifies and quantifies small fragments of cancer DNA circulating in the patient’s bloodstream, known as circulating tumor DNA or ctDNA.

In this study, the scientists successfully analyzed up to 115 mutations per patient in 80 plasma samples from 33 women with stage I to III breast cancer.

Before treatment, TARDIS detected ctDNA in all patients with 0.11% median allele fractions (AF). After completion of neoadjuvant therapy, the researchers observed lower ctDNA concentrations in patients who achieved pathological complete response (pathCR) compared to patients with residual disease (median AFs, 0.003 and 0.017%, respectively, P = 0.0057, AUC = 0.83). In addition, patients with pathCR showed a larger decrease in ctDNA concentrations during neoadjuvant therapy.

The results furter showed that to TARDIS detected ctDNA in as low as 2 parts per 100,000 in patient blood.

“By precisely measuring ctDNA, this test can detect the presence of residual cancer, and inform physicians if cancer has been successfully eradicated by treatment,” explained Muhammed Murtaza, MBBS, Ph.D., Assistant Professor and Co-Director of TGen’s Center for Noninvasive Diagnostics.

Murtaza also holds a joint appointment on the Research Faculty at Mayo Clinic in Arizona, and is one of the study’s senior authors.

based on the study results, the researchers concluded that TARDIS is precise enough to decern if early stage breast cancer patients have responded well to pre-operative, neoadjuvant, drug therapy. It is more sensitive than the current method of determining response to drug therapy using imaging.

“This has enormous implications for women with breast cancer. This test could help plan the timing and extent of surgical resection and radiation therapy after patients have received pre-operative, neoadjuvant, therapy,” said Barbara A. Pockaj, MD, a surgical oncologist who specializes in breast and melanoma cancer patients at Mayo Clinic in Arizona, and is the study’s other senior author.

Pockaj is the Michael M. Eisenberg professor of surgery and the chair of the Breast Cancer Interest Group (BIG), an international collaboration which includes researchers at Mayo Clinic, TGen and ASU.

A simple blood draw
Unlike traditional biopsies, which only produce results from one place at one time, liquid biopsies use a simple blood draw, and so could safely be performed repeatedly, as often as needed, to detect a patient’s disease status.

“TARDIS is a game changer for response monitoring and residual disease detection in early breast cancer treated with curative intent. The sensitivity and specificity of patient-specific TARDIS panels will allow us to tell very early, probably after one cycle, whether neo-adjuvant (before surgery) therapy is working and will also enable detecting micro-metastatic disease and risk-adapted treatment after completing neo-adjuvant therapy,” noted Caldas, who is also a Senior Group Leader at the Cancer Research UK Cambridge Institute, and one of the study’s contributing authors.

Routine monitoring
Following further clinical testing and trials, TARDIS could someday be routinely used for monitoring patients during cancer treatment, and discovering when patients are essentially cured and cancer free.

“The results of these tests could be used to individualize cancer therapy avoiding overtreatment in some cases and under treatment in others,” Murtaza added.

“The central premise of our research is whether we can develop a blood test that can tell patients who have been completely cured apart from patients who have residual disease. We wondered whether we can see clearance of ctDNA from blood in patients who respond well to pre-surgical treatment,” he said.

Current methods
Studies with longitudinal analysis of ctDNA has demonstrated great promise for monitoring treatment response. But existing tests and imaging methods lack adequate sensitivity for residual disease detection during or after completion of treatment in patients with nonmetastatic cancer needed to determine response to treatment.

“Fragments of ctDNA shed into blood by tumors carry the same cancer-specific mutations as the tumor cells, giving us a way to measure the tumor,” said Bradon McDonald, a computational scientist in Murtaza’s lab, and the study’s first author.

“The problem is that ctDNA levels can be so low in non-metastatic cancer patients, there are often just not enough fragments of ctDNA in a single blood sample to reliably detect any one mutation. This is especially true in the residual disease setting, when there is no obvious tumor left during or after treatment,” McDonald said.

“So, instead of focusing on a single mutation from every patient, we decided to integrate the results of dozens of mutations from each patient,” McDonald added.

The study results suggest that personalized ctDNA analysis, using TARDIS, is a promising approach to identifying patients with a curative response following pre-surgical drug therapy.

“Together with imaging and tissue-based predictive biomarkers, ctDNA is rapidly becoming a useful diagnostic test to determine individualized decisions about additional treatment,” Murtaza said.

“We are excited that TARDIS has the potential to really individualize clinical management of patients with non-metastatic cancer,” Pockaj affirmed

Thomas Slavin, M.D., Assistant Clinical Professor at City of Hope National Medical Center, and a contributing author of the study, noted that “reliably identifying, often multiple, circulating tumor mutations in the plasma of patients with non-metastatic breast cancer also holds promise that ctDNA may one day be a great tool for early breast cancer detection.”

TGen is now focused on evaluating the best partners to work with to automate and scale TARDIS, so it can be made available broadly to benefit patients in need.

“This data represents an exciting strategy to improve the sensitivities of liquid biopsies, which have been challenging for breast cancer,” said Karen Anderson, M.D., Ph.D., a researcher at the Biodesign Institute, a medical oncologist at Mayo Clinic in Arizona, and one of the study’s contributing authors.

“This work represents highly collaborative efforts across multiple institutions, and with the generosity and foresight of our patients who have contributed to this study,” Anderson observed.

Patient samples for this study were collected at Mayo Clinic, at Addenbrookes Hospital at the University of Cambridge, and at City of Hope.[1]

* This research was funded by the National Cancer Institute, Mayo Clinic Center for Individualized Medicine, the V Foundation for Cancer Research, Science Foundation Arizona, The Ben and Catherine Ivy Foundation, SmartPractice, Cancer Research UK, City of Hope and TGen.

References
[1] McDonald BR, Contente-Cuomo T, Sammut SJ, Odenheimer-Bergman A, Ernst B, Perdigones N, Chin SF, et al. Personalized circulating tumor DNA analysis to detect residual disease after neoadjuvant therapy in breast cancer. Sci Transl Med. 2019 Aug 7;11(504). pii: eaax7392. doi: 10.1126/scitranslmed.aax7392. [Pubmed][Article]