Federal Grant helps TGen Refine Cancer-detection Blood Tests for Breast Cancer Patients

Muhammed Murtaza, M.B.B.S., Ph.D., Assistant Professor and Co-Director of TGen’s Center for Noninvasive Diagnostics. Courtesy: 2019 TGen. Used with permission.
Muhammed Murtaza, M.B.B.S., Ph.D., Assistant Professor and Co-Director of TGen’s Center for Noninvasive Diagnostics. Courtesy: 2019 TGen. Used with permission.

Scientists at Arizona-based Translational Genomics Research Institute (TGen), an affiliate of City of Hope, have created a new “liquid biopsy” blood test for the early detection of cancer. The test, designed to precisely detected cancer and monitor treatment response, has shown to be viable in laboratory settings. Following confirmation of the viability of the test, a new $2.1 million federal grant will now enable scientists at TGen and Mayo Clinic to fine-tune the test in clinical trials.

Earlier studies have confirmed that this test, called TARgeted DIgital Sequencing or TARDIS, is about 100 times more sensitive than other blood-based cancer monitoring tests.

TARDIS detects cancer by identifying and quantifying small fragments of cancer DNA circulating in the patient’s bloodstream, known as circulating tumor DNA or ctDNA. The development has been met with growing interest in the medical community in using TARDIS to see how well a patient with cancer responds to treatment.

Although the analysis of ctDNA has shown promise for monitoring treatment response, the majority of current methods lack adequate sensitivity to detect residual disease during or after completion of treatment in patients with nonmetastatic cancer.  With the development of the TARDIS test, the scientists at TGen and Mayo Clinic addressed this problem and improved the sensitivity for minute quantities of residual tumor DNA in plasma. [1]

Guiding treatment
Reliable performance of blood tests can be affected by sample handling.

The $2.1 million, 5-year grant from the National Cancer Institute (NCI) will enable TGen and Mayo Clinic scientists to evaluate the impact of pre-analytical factors on liquid biopsies, such as blood collection tubes, DNA extraction methods, and long-term storage of ctDNA results and analysis.

“Circulating tumor DNA analysis can guide treatment of patients with localized cancers, and metastatic cancers that spread to other body organs,” said Muhammed Murtaza, M.B.B.S., Ph.D., Assistant Professor and Co-Director of TGen’s Center for Noninvasive Diagnostics. He holds a joint appointment on the Research Faculty at Mayo Clinic in Arizona and is a senior author of a study published August 7, 2019 edition of Science Translational Medicine, which suggests TARDIS can detect ctDNA in as low as 2 parts per 100,000 in patient blood.[1

This interpretation is important. For example, in results from a study published in Science Translational Medicine demonstrated that after completion of neoadjuvant therapy, ctDNA concentrations were lower in patients who achieved pathological complete response (pathCR), defined as the absence of residual invasive and in situ cancer, compared to patients with residual disease (median allele fractions [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. [1]

Murtaza and his co-authors concluded that these results demonstrate high accuracy for assessment of molecular response and residual disease during neoadjuvant therapy using ctDNA analysis, conforming that personalized ctDNA tracking could enable individualized clinical management of patients with cancer treated with curative intent.[1]

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

Hence, being minimally invasive and less complicated, liquid biopsies holds clear advantages over traditional biopsies. [2]

“However, pre-analytical factors such as blood collection tubes, processing protocols and storage conditions can affect the outcome of molecular tests,” Murtaza said.

Earlier stages
“Besides looking at how blood processing affects the ctDNA results in patients with localized breast cancer, this new project allows us to investigate how well ctDNA analysis performs in even earlier stages of breast cancer than we have described previously,” explained Barbara A. Pockaj, MD, a surgical oncologist who specializes in breast and melanoma cancer patients at Mayo Clinic in Arizona.

Pockaj, who is the other senior author of the article published in Science Translational Medicine, is the Michael M. Eisenberg professor of surgery and the chair of the Breast Cancer Interest Group (BIG), a collaboration between researchers at Mayo Clinic, TGen and Arizona State University (ASU).

Circulating tumor DNA
The ctDNA levels are much lower in patients with localized cancer than in those with metastatic cancer.

Across different clinical and research sites, there can be many differences in sample handling, such as differences in blood collection and processing, and DNA extraction.

For example, delays in processing a blood sample after collection can cause a dilution or degradation of ctDNA in blood samples. In early stage cancer patients, where ctDNA levels are already quite low, this could cause false-negative results.

To address this, scientists at TGen and Mayo Clinic will study 180 patients with early and locally advanced breast cancer to investigate three aspects of pre-analytical variation: DNA extraction methods, blood collection tubes and processing protocols, and long-term storage of plasma and extracted DNA.

“There is a lot of potential in ctDNA analysis to enable early detection of cancer and residual disease detection in treated patients,” Murtaza noted.

“However, there is still no agreement in the field on the best way to process blood samples prior to any analysis. With support from the Cancer Diagnosis Program at the National Cancer Institute, this project will try to address some of these long-standing questions in the field, particularly for early stage cancer patients, where such factors can completely change the interpretation of results,” he concluded.

Reference
[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]
[2] Ilié M, Hofman P. Pros: Can tissue biopsy be replaced by liquid biopsy? Transl Lung Cancer Res. 2016 Aug;5(4):420-3. doi: 10.21037/tlcr.2016.08.06.[Pubmed][Article]