1.  How does your work relate to the OvaCheck™ test for ovarian cancer being developed by private industry?

The U.S. Food and Drug Administration (FDA)/National Cancer Institute (NCI) Proteomics Program is not involved with the development of the OvaCheck™ test. The OvaCheck™ test is being independently developed by Correlogic Systems in conjunction with Quest Diagnostics and LabCorp, two non-governmental, private companies. Neither the NCI nor FDA has been involved in the design or validation of OvaCheck™ methodology. Additionally, the data posted or published by the NCI/FDA program can not be used to assess or judge tests developed using different technology.

The OvaCheck™ test is unrelated to previously published work between Correlogic and the NCI/FDA, and utilizes different mass spectrometry instrumentation and detection methods, as well as different sample handling and processing methods. A mass spectrometer works by using magnetic and electric fields to exert forces on charged particles (ions) in a vacuum. Therefore, a compound must be charged or ionized to be analyzed by a mass spectrometer.

The OvaCheck™ test employs electrospray ionization (ESI) type of mass spectrometry using diluted denatured blood samples, whereas the NCI/FDA group uses matrix-assisted laser desorption ionization (MALDI) analysis of undiluted native blood serum. The class of molecules analyzed by these two approaches, and thus the molecules that constitute the diagnostic patterns, would be expected to be entirely different. Specifically, the ion spectra mass/chare values in the published or posted NCI /FDA data are not directly comparable to the data derived from OvaCheck™, which uses a different technology.

However, a research collaboration does exist between scientists from FDA, NCI, and Correlogic Systems. These scientists are productively collaborating on research studies to identify MALDI-based patterns of protein expression related to specific disease states, including ovarian cancer, using Correlogic's proprietary software. These research studies are distinct from Correlogic's development of the OvaCheck™ test.

Scientists at FDA and NCI cannot comment on the work being done independently by Correlogic (and specifically OvaCheck ™) since they are not involved with, nor are they privy to, proprietary corporate data.

2.  Is the NCI/FDA Proteomics Program developing a test for the detection of ovarian cancer of their own?

Neither the NCI nor the FDA is conducting research to develop a "test" for the detection of ovarian cancer. The NCI/FDA Proteomics Program is conducting a series of research studies to examine the hypothesis that proteomic patterns are different in cancer versus control samples. Currently the program is working to refine, improve, and optimize its techniques, to validate the test results, and to identify and sequence the diagnostically important molecules which underpin mass spectrometry readings (Mass spectrometry is the tool that is used to distinguish one protein from another by virtue of differing molecular weights and electrical charges).

The NCI/FDA Proteomics Program is not currently, and has not previously, worked on the development of a commercial test to be used in patients to detect ovarian cancer. Neither is it involved in the marketing of any early detection tests.

3.  You are looking for biomarkers that are diagnostic for cancer. Doesn't that mean you are developing a test for earlier detection of cancer?

The NCI/FDA research is not yet to the stage of developing, validating, and marketing a diagnostic test for use in patients. NCI/FDA scientists are currently validating their techniques, analyzing data, repeating experiments, and optimizing methods. These are all research activities that must be done in a deliberate, step-wise progression and must be rigorously validated before a diagnostic tool or treatment could be developed.

The FDA/NCI researchers' paper, published in The Lancet in February, 2002, was a feasibility study. It described an approach, whereby mass spectrometry generated fingerprints (unique identifiers) derived from low molecular weight molecules could discriminate between a study set of ovarian cancer tumors and specimens from healthy high risk women. Neither the paper, nor the molecules described were the basis of any test; rather they were a description of an approach. Since this publication, this new approach has shown promising results in a wide variety of cancers and other diseases by many laboratories and investigators throughout the world.

Additionally, a prospective clinical trial to stringently test the hypothesis would have to be designed and completed prior to development and marketing of a diagnostic.

4.  What is the National Cancer Institute/U.S. Food and Drug Administration Clinical Proteomics Program?

The collaboration between the NCI and the FDA began in 1997, and is led by Lance Liotta, M.D. Ph.D., of NCI's Center for Cancer Research, and Emanuel Petricoin, Ph.D., of FDA's Center for Biologics Evaluation and Research (CBER).

The scientific goal of proteomics is to understand the flow of information within the cell and the organism. Petricoin and Liotta have created new technologies to analyze the molecular networks of diseased cells, These technologies include the use of tissue biopsy specimens to develop tools for protein fingerprinting of body fluids and tissue. Potential benefits of clinical proteomics include developing individualized therapies using targeted treatments that could be predetermined to be effective for each patient; determining the toxic and beneficial effects of treatments in the lab before using them in patients; potentially diagnosing cancer earlier than is now possible; and improving the understanding of tumors at the protein level, possibly leading to better treatments.

Through the Clinical Center at the National Institutes of Health, Elise Kohn, M.D., of NCI, uses a special Laser Capture Microdissection Microscope (LCMM) to analyze cells biopsied from cancer patients (before and after treatment). LCMM was invented in Liotta's laboratory. The microscope allows the isolation of pure normal cells, pre-cancerous cells, and tumor cells from the same patient. By capturing cells directly from the tissue, the original protein pattern of the cells is maintained, which is not the case with traditional methods of isolating cells.

The scientists are also analyzing the molecular network, or the cellular "circuitry", of cancer cells from a biopsy specimen using new types of protein microarrays and a large panel of validated antibodies that specifically recognize proteins that are phosphorylated (have a phosphorus molecule attached to them). For example, researchers are studying how a particular treatment changes the network, or circuitry, of proteins in a cell. They are also looking for signaling pathway changes if a tumor returns after treatment.

One such example is a NCI phase II trial of the drug Gleevec in relapsed ovarian cancer patients, which is open for accrual.

5.  What additional proteomics research done by Drs. Liotta, Petricoin and Kohn is contributing to the current proteomics tools being evaluated by them and what is planned next?

Pivotal to the ongoing and most recent development of the proteomics pattern approach reported in various manuscripts by Liotta and Petricoin was the discovery that low-molecular weight proteins, metabolites, and peptides useful for early detection of ovarian cancer accumulate on larger, highly abundant carrier proteins in the blood such as albumin. This piggy-backing ensures that the smaller molecules are enriched and have a longer life in the circulating blood (Liotta L, et al, Nature, Oct. 2003, "Written in Blood" and Mehta AI, et al., Disease Markers, Dec 2003, "Biomarker amplification by serum carrier protein binding"). Knowing this, researchers can obtain a greater concentration of potential biomarker proteins by extracting the carrier protein fraction from the blood. Scientists from the NCI/FDA Clinical Proteomics Program are working with Mauro Ferrari, Ph.D., a world-renowned nanotechnology expert, to create synthetic nanoparticles that can act like carrier proteins which could be used to further enrich diagnostic protein patterns.

Although it is not necessary, in theory, to know the identity of the proteins that prove to be useful to detect early disease or response to treatment, many of these low molecular weight proteins are bound to a carrier protein and have now been identified. This discovery is leading to an understanding of the molecular pathways involved in disease states. These efforts are also leading to the discovery of many new protein biomarkers in the blood. The NCI/FDA investigators are also working towards developing approaches in which proteins are used as sample material for high throughput immunoassay or mass spectrometry fingerprinting.

Besides ovarian cancer, similar techniques are being applied to other cancers. The researchers are looking for protein patterns and identified carrier protein-bound molecules in the blood that are diagnostic for early-stage aggressive prostate, lung, and breast cancers, as well as patterns that can predict risk for prostate, colon, skin, and pancreatic cancers.

In addition to analyzing proteins in the blood, another thrust of the proteomics program is to use new types of protein microarrays developed by the NCI/FDA investigators to compare the proteins in tumor tissue vs. healthy tissue. Using this approach, researchers are probing tissues for phosphorylated proteins known to be important in cellular signaling events which are very often targets for therapy. These arrays can provide information about the activity of many signaling pathways simultaneously, thereby providing insights into mechanisms of cancer development and tumor progression. The work is yielding new insights about which molecular pathways are altered in tumor development, and may lead to strategies for patient-tailored therapy.

The general strategy of the proteomics program is to analyze proteins from the blood or tissue with mass spectrometry and protein microarrays to identify important changes related to disease. The ultimate goal is to use this information for earlier detection of cancer, patient-tailored therapy, and more effective therapeutic monitoring.. NCI/FDA experts are continuing to test alternative mass spectrometry platforms, sample preparation and fractionation methods, protein microarray technology, nanotechnology systems, and computer algorithms to improve and extend the ongoing research.

6.  What are biomarkers and how are they developed?

Successfully translating research on biomarker applications from the laboratory to patients involves five phases: