New test to detect rare proteins in blood

Applications of new method will make possible earliest warning of cancer and other diseases

Researchers at the University of Pennsylvania School of Medicine have developed a paradigm-shifting method for detecting small amounts of proteins in the blood. Applications of this method will make discerning low-abundance molecules associated with cancers (such as breast cancer), Alzheimer’s disease, prion diseases, and possibly psychiatric diseases relatively easy and more accurate compared with the current methodology, including the widely used ELISA (enzyme-linked immunoadsorbent assay).
ELISA is a common immune-system-based assay that uses enzymes linked to an antibody or antigen as a marker for picking out specific proteins. For example, it is used as a diagnostic test to determine exposure to infectious agents, such as HIV, by identifying antibodies present in a blood sample.

The sensitivity of detecting molecules by the new method, called FACTT, short for Florescent Amplification Catalyzed by T7-polymerase Technique, is five orders of magnitude (100,000 times) greater than that of ELISA, the Penn researchers found.

Senior author Mark I. Greene MD, PhD, the John Eckman Professor of Medical Science, Hongtao Zhang, PhD research specialist; Xin Cheng, PhD, research investigator, and Mark Richter, a research technician in Greene’s lab, report their findings in the advanced online publication of Nature Medicine.

“The current ELISA tests can only detect proteins when they are in high abundance,” says Zhang. “But the problem is that many of the functional proteins – those that have a role in determining your health – exist in very low amounts until diseases are apparent and cannot be detected or measured at early stages of medical pathology. It was important to develop a technique that can detect these rare molecules to detect abnormalities at an early stage.”

The FACTT technology uses a different enzyme amplification system so quantitative signals can be obtained from even a few protein molecules compared to ELISA. “The technology is remarkably adaptable to any protein and can be performed in an automated format,” notes Greene. He states that the technology will soon be robotized so as to be able to screen for many rare disease-causing proteins using tiny amounts of blood. “It is even possible that one could screen for multiple diseases at the same time and produce a precise accounting of whether disease-causing molecules are present at an early time when disease can be readily treated,” adds Greene.

Greene also noted that the FACTT technology represents the further evolution of an earlier approach that was developed in collaboration with Professor of Pharmacology James Eberwine, PhD, also from Penn. The earlier technique employed radioisotopes.

Development of a test for the cancer marker Her2/neu

The researchers compared detection of Her2/neu in the blood between ELISA and FACTT. Her2/neu proteins were in fact first identified by the Greene laboratory in the early 1980s, and the Her2/neu gene was found by other scientists to be overexpressed in breast cancer. Her2/neu is normally a low-abundance molecule that becomes overexpressed in more than 30 percent of primary breast, ovarian, and pancreatic tumors. Part of the Her2/neu molecule is shed from the surface of tumor cells and has been detected in the blood of breast-cancer patients. Higher blood concentrations of Her2/neu correlate with a lower response rate to chemotherapy and shorter survival time after relapse.

The Greene lab developed mouse models that carry cancer cells overexpressing Her2/neu. When these cells are implanted into animals they form tumors exactly like breast tumors in humans. Using ELISA, the researchers could not detect Her2/neu from mouse blood until the tumors reached an inoperable size, but with the new FACTT technology they could detect Her2/Neu in some mice when tumors were barely visible and within two days of implantation. These results indicate that it is possible to detect tumors at very early stages so that tumor emergence or reoccurrence can be rapidly treated or even prevented.

Greene’s laboratory established many of the principles of targeted therapy for Her2/neu tumors and the prototype antibodies that led to the development of Herceptin, a similar antibody molecule that was created by Genentech. The Greene laboratory also previously showed that early treatment of Her2/neu tumors with targeted monoclonal antibodies in animal models led to far more significant prevention of tumor growth as well as tumor emergence and reoccurrence.

Greene stresses that early treatment is far more effective than treating advanced tumors with the same antibodies. Recent clinical trials support the notion that early treatment prevents tumor reoccurrence in women with breast tumors. FACTT technology represents a way to couple early diagnosis with early treatment to prevent tumor emergence.

Detecting Her2/neu in humans for breast cancer

The most widely used clinical Her2/neu tests are IHC (immunohistochemistry) and FISH (fluorescence in situ hybridization). However, both FISH and IHC are complex, time-consuming tests.

Patients who test positive for Her2/neu using FISH or IHC have responsive rates of about 35 percent to the cancer drug Herceptin. Monitoring Her2/neu status from the blood with a powerful technology such as FACTT represents an alternative approach compared to IHC or FISH, say the researchers.

Pre-treatment Her2/neu levels correlate with tumor size and the extent of disease. Post-treatment Her2/neu levels predict disease-specific survival. A more sensitive assay could more accurately allow treatment of humans with breast cancer and allow treatment more quickly if the tumor reoccurs.

The researchers collected blood samples from healthy women and breast cancer patients who did or did not overexpress Her2/neu, as detected by IHC and FISH. When using the new FACTT method her2/neu positive cancer patients showed dramatically elevated Her2/neu levels (average: 384 ng/ml), while the level in Her2/neu-negative breast cancer patients (19.5 ng/ml) were close to the levels of the healthy control participants (16.6 ng/ml).

Using FACTT, nine out of 10 of the Her2/neu positive patients had elevated Her2/neu levels and one out of four in the Her2/neu negative group had elevated Her2/neu levels. Using ELISA only two out of 10 in the Her2/neu positive group showed elevated Her2/neu levels.

“Clearly the sensitivity of the ELISA assay does not satisfy the current need for the clinical detection of marker proteins that determine whether a patient has breast cancer or not,” says Greene.

The researchers have also tried the FACTT method on other rare, but medically important molecules, such as the prion protein (for mad cow disease with Mansun Sy at Case Western University) and TNF-alpha (for autoimmune diseases), and will be developing tests for other cancer markers including lung cancer and colon cancer. All proteins tested so far with FACTT have been detected with an over 1000-fold higher sensitivity compared to current technologies.

The researchers say this points to FACTT’s broad applicability and compatibility with current high-throughput testing technology. This, in turn, will facilitate the detection of rare markers and not-so-rare targets from much smaller sample volumes, as well as aid in monitoring marker levels at much earlier stages of disease.

“The importance of FACTT is that we can still get an accurate description of the number of molecules that cause disease even when other assays cannot,” says Greene. The researchers surmise that FACTT could be used to monitor levels of Her2/neu in already-diagnosed breast cancer patients to monitor recurrence or treatment effectiveness.

“The critical issue arises when women are diagnosed with early breast cancer,” adds Greene. “They often have a lumpectomy and are sometimes treated with radiation or chemotherapy, but despite this conventional therapy the cancer still can occasionally reoccur,” says Greene. Detection of very early recurrence is important and Greene feels the power of this technology will facilitate recognizing early phases of tumor emergence.

Rational targeted therapy has shown in animal models – over 10 years ago – and more recently in clinical trials that treatment of small or incipient tumors is a way to prevent tumor emergence or reoccurrence. “Prevention of the consequences of recurrence is critical since treating advanced tumors is very complex and difficult,” concludes Greene.