New liquid biopsy test can quickly identify cancerous DNA in patients with metastatic breast cancer

A new automated liquid biopsy test being developed by researchers at Johns Hopkins Kimmel Cancer Center can accurately detect the presence of cancerous DNA in the blood of patients with metastatic breast cancer within five hours. The test, currently a prototype for research use only, could potentially be used to quickly help oncologists determine if cancer treatments work.

The test, called Liquid Biopsy for Breast Cancer Methylation (LBx-BCM), is compatible with a commercially available molecular testing platform called GeneXpert® and can detect methylation, a type of chemical tag, in one or more of nine genes altered in breast cancers within 4.5 hours. It requires less than 15 minutes hands-on time by a lab technician. A validation of the test and its potential uses was published online May 6 in the journal Cancer Research Communications.

Many breast cancer patients do not respond to chemotherapy, but go through several rounds of treatment before oncology teams can perform imaging studies to determine if a treatment is working, says the author. study principal, Saraswati Sukumar, Ph.D., professor of oncology and pathology at Johns Hopkins University School of Medicine. Imaging can be effective at detecting changes in larger tumors, but identifying changes in smaller tumors is nearly impossible, Sukumar says.

Our goal was to develop a test that would be sophisticated yet simple to perform worldwide and could be used at the point of care to provide same-day feedback to clinicians and patients. If we are able to show through this cartridge test that we are indeed successful in predicting the course of treatment, we may be able to institute changes in the way we view chemotherapy and the way we treat patients with of metastatic breast cancer.

Saraswati Sukumar, Ph.D., Professor of Oncology and Pathology, Johns Hopkins University School of Medicine

With the LBx-BCM test, developed in collaboration with Cephied scientists, a technician can place blood or plasma samples from cancer patients into tubes containing a reagent, a mixture used to extract DNA, and place the contents in cartridges for the commercial system to chemically modify the DNA, then amplify and detect the methylated genes, quickly returning the results. The test looks for methylation markers (chemical alterations in DNA unique to cancer cells) among a panel of nine genes that recognize the four subtypes of breast cancer. The genes are AKR1B1, TM6SF1, ZNF671, TMEFF2, COL6A2, HIST1H3C, RASGRF2, HOXB4 and RASSF1.

The Johns Hopkins team previously developed a liquid biopsy laboratory test called cMethDNA, which identified the presence of hypermethylation among 10 altered genes in breast cancers. Hypermethylation is a chemical alteration of DNA that often silences the function of genes that control uncontrollable cell growth. Its appearance in the DNA of breast cancer-related genes shed in the blood indicates that the cancer has come back or has spread. The test can detect up to 90% of patients with metastatic breast cancer and can help predict treatment response and long-term patient outcomes. However, it takes 10 days and requires a high degree of technical skill. LBx-BCM builds on that work, and because it’s automated, takes much less time, says Mary Jo Fackler, Ph.D., the study’s lead author.

To test LBx-BCM, investigators first had two people perform the test on different days, using stored samples from 11 patients with metastatic breast cancer and four without breast cancer. The results were the same for more than 90% of the cases.

They also investigated the test’s ability to detect metastatic breast cancer in two sets of samples from previous studies at Johns Hopkins. They looked at the cumulative methylation of the nine genes in 20 serum samples from patients with metastatic breast cancer and 20 from people without breast cancer. A second set of samples from 40 people with metastatic breast cancer, 17 with benign breast disease and nine without breast cancer, were analyzed. In both series, LBx-BCM detected two to 200 times more methylated DNA in plasma samples from people with breast cancer than in normal or benign samples.

The test was found to correctly detect cancer 83% of the time and correctly exclude cancer 92% of the time, for an overall diagnostic accuracy of 85%.

“Further prospective clinical trials will evaluate the detection sensitivity of LBx-BCM and its ability to monitor therapeutic response during the treatment of advanced breast cancer,” Sukumar and colleagues wrote.

In addition to Sukumar and Fackler, other researchers were Claudia Mercado-Rodriguez, Leslie Cope, Bradley Downs, Abdul Hussain Vali, Jennifer Lehman, Rita Denbow, Jeffrey Reynolds, Morgan Buckley, Kala Viswanathan, Christopher Umbricht, Antonio Wolff, and Vered Stearns of Johns. Hopkin; Suzana Tulac, Neesha Venkatesan, Adam Aslam, Timothy de Guzman, Michael Bates and Edwin Lai of Cepheid, Sunnyvale, CA; and Wanjun Ding from Renmin Hospital of Wuhan University, China.

The work was supported by the Department of Defense (grant W81XWH-18-1-0018) and a research agreement from Cepheid.

Sukumar, Fackler and Wolff are the inventors of the cMethDNA test, US patent US10450609B2, and have also obtained international patents filed with Johns Hopkins University.


Journal reference:

Fackler, M.J. et al. (2022) Development of an automated liquid biopsy test for methylated markers in advanced breast cancer. Communications on cancer research.


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