Posted July 2, 2014
Saraswati Sukumar, Ph.D., Johns Hopkins University

Saraswati Sukumar, Ph.D. The molecular mechanisms underlying the development and progression of breast cancer remain poorly understood. What is clear, however, is that its initiation and progression are the result of genetic errors that adversely affect important cellular processes such as cell cycle control, DNA repair, and cell death pathways. Cancer initiation occurs when these gathering mutations cause either the inactivation of tumor suppressor genes or, conversely, the activation of proto-oncogenes.

Mutations to the DNA sequence have long been studied for their role in turning a normal cell into a tumor cell. But over the past decade and a half, it has become clear that other alterations to the genome, independent of DNA sequence, play at least an equally important role in cancer development. Dr. Saraswati Sukumar, at Johns Hopkins University, and her colleagues have exploited one of these sequence-independent alterations to create a test that can detect metastatic breast cancer with an efficiency better than any test being currently used. The test, she predicts, will also monitor a patient’s response to treatment far more quickly than conventional tests and may allow doctors to adjust treatments and in this way minimize patient exposure to ineffective treatments. Amazingly, the test, developed by Dr. Sukumar with Breast Cancer Research Program support from an FY03 Center of Excellence Award, detects breast cancer by sampling the patient’s blood.

The key alteration is DNA methylation. Not all genes are active all the time, and one way a gene can be silenced is through the attachment of methyl molecules to the gene’s promoter region – the part of a gene that controls where and to what extent a gene is activated. As researchers are now finding out, there are many ways in which this otherwise normal method of gene repression can tip the balance from a gene network that functions normally to one that is cancerous.

As Dr. Sukumar explains, the importance of a blood-based test is twofold. “There are two urgent needs right now. First is the detection of the recurring cancer as metastasis. And second is evaluation of treatment response in a patient diagnosed with metastatic cancer. There is no simple yearly test that can reliably tell a survivor of breast cancer that she is doing well, or that the cancer is coming back. That is the goal we are working towards.”

In work spearheaded by co-investigator Dr. Mary Jo Fackler, Dr. Sukumar and colleagues developed such a test, called “cMethDNA,” a multiplexed PCR assay that measures the level of methylation in 10 genes known to be hypermethylated in breast cancer. In pilot studies, cMethDNA detected metastatic breast cancer from the blood serum of patients, with higher than 90% sensitivity and specificity.

Currently, the onset of symptoms such as ache in the bones, shortness of breath, headaches, or pain, alerts a patient’s oncologist that the breast cancer may have spread to other sites. Dr. Sukumar thinks that the disease at this point may be too advanced to treat effectively. “There is an urgent need for a blood test that will provide a clean bill of health each year, or let the patient and doctor know if the tumor is coming back. It is possible that finding metastasis earlier will lead to changes in treatment strategies in the future. We are working steadily towards devising such a test.”

A number of technologies are already in development to detect and track breast cancer during treatment, and Dr. Sukumar poses the question, “So why use our test?” Her answer: “Our pilot studies show that the cMethDNA test can detect changes very rapidly, say within 3 weeks of treatment initiation. Tumor shrinkage cannot be that rapidly detected by imaging. In the study, when patients responded to treatment, the levels of methylation dropped within 3 weeks of treatment. When they did not respond to treatment, the methylation levels in serum stayed the same or increased. A less expensive test that can be conducted at weekly intervals throughout the treatment period may provide distinct advantages.”

Right now only a small handful of tests targeting DNA methylation to detect cancer have reached the market, even though methylated genes are the most common epigenetic alteration discovered in breast cancer. And, as cMethDNA is still in the early stages of development, it will be some time before the assay might be used in the clinic. Nonetheless, Dr. Sukumar and her team consisting of medical oncology, biostatistics and bioinformatics experts are wasting no time in making that moment a reality. “The next step is to validate the assay in an independent sample set collected in a trial designed for this purpose (a prospective trial), a set we have recently tested by cMethDNA. If the data obtained through such analysis is promising, this bodes well for the assay and brings it closer to the clinic. Also, at this stage, it is important to automate the assay. Automation allows the machine to perform all the steps of the assay, removing human error and effort in the laboratory, and, at the same time, allowing the assay to be used in remote locations. We are currently looking for collaborations with commercial entities for this purpose.”


Fackler MJ, Lopez Bujanda Z, Umbricht C, Teo WW, Cho S, Zhang Z, Visvanathan K, Jeter S, Argani P, Wang C, Lyman JP, de Brot M, Ingle JN, Boughey J, McGuire K, King TA, Carey LA, Cope L, Wolff AC, Sukumar S. 2014. Novel methylated biomarkers and a robust assay to detect circulating tumor DNA in metastatic breast cancer. Cancer Research 15;74(8):2160-2170.

Top of Page


Public and Technical Abstracts: Public and Technical Abstracts: Center of Excellence in Molecular Targeting of Breast Cancer Metastasis