Personalized Blood Test Can Track Tumor-Specific Markers After Therapy

[Hopeful]

SAN DIEGO (EGMN) - Scientists have developed a new way to track cancer using DNA-based blood tests to monitor individualized biomarkers after treatment of solid tumors, and thereby to detect cancer recurrence, an advance that could further the personalized management of cancer patients.

The method, known as PARE (Personalized Analysis of Rearranged Ends), "is based on next-generation mate-paired analysis of resected tumor DNA to identify individualized tumor-specific rearrangements," researchers led by Dr. Victor Velculescu explained in a study scheduled to be published on Feb. 24 in Science Translational Medicine. "Such alterations are used to develop [polymerase chain reaction-based] quantitative analyses for personalized tumor monitoring of plasma samples or other bodily fluids."

During a press briefing at the annual meeting of the American Association for the Advancement of Science, one of the study's authors, Dr. Luis A. Diaz Jr., said that PARE "allows us to measure the amount of cancer DNA in any clinical specimen. As soon as a patient's cancer is identified by biopsy, it can be scanned for gene rearrangements. These rearrangements will then be a template to act as a fingerprint for that individual cancer. This can be applied in a variety of clinical scenarios."

Dr. Velculescu, codirector of the cancer biology program at Johns Hopkins Kimmel Cancer Center in Baltimore, and his associates used six sets of tissue samples obtained from four patients with colorectal cancer and two patients with breast cancer to catalog the number of gene sequences in each patient. They did this by first identifying regions where the number of DNA sequences was more or less than anticipated and where sections of different chromosomes fused together.

The researchers then analyzed these regions further to identify DNA sequences that displayed incorrect ordering, orientation, or spacing, and observed that an average of 9 rearrangements was found in each of the six samples (range, 4-17).

"The rearrangements represent the most dramatic form of genetic changes that can occur in the genome," Dr. Velculescu said at the briefing. "If the genome were like a book with many chapters, the rearrangement would be like swapping of two chapters within book, so that both chapters would be out of order. If one could recognize rearrangements accurately, that could potentially be one of the best ways to distinguish cancer cells from normal cells."

Next, they looked for the same changes as shed from tumors into the blood of patients. After amplifying DNA that was found in the blood of two of the colorectal cancer patients, they determined that the tests were robust enough to detect rearranged tumor DNA.

For example, the fraction of mutant DNA contained in the blood of one of the colorectal cancer patients was 37% prior to surgery for tumor removal, and it dropped to 14% after surgery. "The mutant DNA fraction decreased further after chemotherapy and subsequent removal of metastatic lesions from the right lobe of the liver," the researchers reported. "However, the fraction of mutant tumor DNA did not reach zero (remaining at 0.3% at day 137), consistent with the fact that this patient had residual metastatic lesions in the remaining left lobe of the liver."

The researchers noted certain limitations of the study, including the chance that some rearranged genetic sequences "could be lost during tumor progression," and that the PARE assay currently costs about $5,000, making it expensive for general clinical use. "This cost is a consequence of the high physical coverage and the inefficiencies associated with stringent mapping of 25-bp sequence data to the human genome," the researchers explained.
"As read quality and length continue to improve, less stringent mapping criteria and lower physical coverage will permit analyses similar to those in this study but with substantially less sequencing effort. Moreover, the cost of massively parallel sequencing, which has decreased substantially over the last 2 years, continues to spiral downwards."

Despite such limitations, Dr. Velculescu and his associates maintain that the potential applications for PARE are "numerous," including the identification of tumor-free surgical margins, the analysis of regional lymph nodes, and the measurement of circulating tumor DNA after surgery, radiation, or chemotherapy. "Short-term monitoring of circulating tumor DNA may be particularly useful in the testing of new drugs, as it could provide an earlier indication of efficacy than possible through conventional diagnostic methods such as computed tomography scanning," they concluded.

At the briefing, Dr. Diaz, an oncologist at Johns Hopkins, said that PACE could be used to help clinicians determine who is cured or not cured after surgical resection. "Currently, as physicians we can't tell a patient after breast, colon, or lung cancer surgery whether or not they've been cured," he commented. "A fraction of these patients will be cured by surgery alone, but many will have residual disease. We hope that PARE will be able to discriminate between those individuals that are cured and those that are not cured by detecting residual disease at first surgery. This approach would thereby spare cured individuals from unnecessary and potentially toxic and harmful chemotherapy."

Under a licensing agreement between the Johns Hopkins University and Genzyme Corp., three of the investigators, including Dr. Velculescu, are entitled to a share of royalties received by the university on sales of products related to research described in the study.

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