Proteomic Tests Poised For Clinical Market

Potential for earlier detection, higher sensitivity and specificity

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CEO SUMMARY: Proteomics-based technology is developing rapidly. The strategic collaboration announced last month between Ciphergen Biosystems and Quest Diagnostics Incorporated is potentially worth $25 million. It is an expensive bet that next-generation proteomics tests soon to enter the clinical marketplace will provide high clinical utility and give physicians new diagnostic tools.

NEW PROTEOMIC-BASED TECHNOLOGIES ARE MOVING STEADILY toward the clinical diagnostics marketplace. The promise of proteomics is highly sensitive, multi-analyte assays capable of early detection of disease.

Competition to establish market advantage in proteomics-based diagnostic testing is intensifying. One example is the $25 million deal between Quest Diagnostics Incorporated and Ciphergen Biosystems, Inc. to commercialize selected assays from Ciphergen’s proteomics pipeline. (See TDR, August 1, 2005.)

Prime Time For Proteomics?

The high level of interest in novel proteomics assays by major players is one sign that a market shift is under way. For that reason, it is timely for pathologists and lab executives to look at why Quest Diagnostics and Ciphergen think their $25 million deal makes economic sense—and whether this particular technology has the potential to shift the testing paradigm within the clinical laboratory industry.

The diagnostic potential of proteomics is huge. That’s because of ongoing discoveries involving the role of proteins in disease. Many proteins undergo post-translational biochemical changes. These changes create enzymes which modify or cleave the proteins in a specific way. Proteomic techniques now under development permit large-scale quantitative comparisons between normal and diseased cells in these post-translational protein expressions. Ciphergen, along with serveral other biotech firms, is targeting this area of diagnostic potential.

“Proteomics technologies used today permit large-scale quantitative comparisons between disease and disease-free clinical samples,” observed Eric T. Fung, M.D., Ph.D., Vice President of Clinical Affairs at Ciphergen, based in Fremont, California. “The goal of today’s translational proteomics is to discover novel biomarkers and combinations of biomarkers to determine which such markers are indicative of distinct dis- ease conditions.”

Ciphergen’s technology is called SELDI, for “Surface-Enhanced Laser Desorption/Ionization.” It is a proprietary proteomics system which uses proprietary ProteinChip® arrays. These arrays are specifically designed to discover, validate, and analyze different biomarkers.

“Many people think we ‘discover’ with SELDI and ‘validate’ on ELISA (Enzyme-Linked Immunosorbent Assay),” observed Fung. “However, SELDI allows researchers to go directly from discovery to assay. Not only does this speed up the process, but it allows measurements in real time.

Multi-analyte Assays

“SELDI also allows us to simultaneously analyze multiple analytes,” explained Fung. “This is a needed capability in pharmacogenomics, or personalized medicine.”

Ciphergen is using SELDI-based processes and associated bioinformatics tools to generate multi-marker assays. It is working on tests to better classify four different types of cancers—breast, ovarian, colon, and prostate. “The SELDI platform uses the body’s host response as an amplified signal,” noted Fung. “This allows detection of even very small tumors. We have termed this response ‘host response protein amplification cascade,’ or HRPAC.”

High-throughput System

“The key to proteomics is separation,” stated Gail Page, Ciphergen’s President and Chief Operating Officer. “We have developed systems and processes that provide for high through- put, parallel-fashion protein separation. It marries robotics and automated liquid handling in a 96-well format. Knowing that the eventual market for this product will be clinical laboratories, it is designed with throughput and reproducibility of outcomes in mind.”

“SELDI affords Ciphergen the unique capability of creating a strong pipeline of research assays,” explained Page. “Most small diagnostic companies typically enter the market based on their development of a single clinical assay. We are not constrained by that limitation.

Research Versus Clinical

“What gives our technology a special advantage is that the entire process of discovery and analysis can be per- formed on the same platform,” observed Page. “We believe this will accelerate the time from assay discovery and validation to clinical use.”

As an example, it took a year or more for new generations of gel technology to move from research labs to clinical labs. Ciphergen believes its sophisticated software will allow its proteomics-based assays to make the transition from research into clinical use in a matter of months.

“Now, with our sophisticated software, we believe these proteomics-based assays can make the transition from research into clinical use in a matter of months.”

“Biomarker tests are quantitative measurements of biological activity that signal the presence of disease,” said Fung. “Multi-marker assays are the basis for the clinical diagnostic tests that Ciphergen is preparing.” In the pipeline are proteomic-based tests being developed for use by the physician in the management of ovarian, breast, liver and prostate cancers.

“Researchers are identifying bio- markers for cardiovascular disease, Alzheimer’s disease, and other neurodegenerative diseases,” he added.

“Other areas of current research for Ciphergen include infectious diseases and blood bank testing.”

Ciphergen has strategic alliances with two key players in clinical diagnostics. In June 2005 Ciphergen entered into a research collaboration with Bayer Pharmaceuticals Corporation to identify biomarkers predictive of response to cancer therapy, and to develop assays for cancer clinical trials.

A month later, in July, Ciphergen signed an agreement with Quest Di- agnostics. “We see a philosophical alignment between our two companies,” commented Page. “There is a shared vision of growth through new technology and novel assays.

Access To Clinical Market

“In particular, we see Quest as an innovator, backed by good marketing and focused on good science,” she explained. “Over the years they have demonstrated experience in launching new clinical assays. As we move our assays from the development stage to the commercialization stage, this alliance with Quest Diagnostics gives us access to the clinical marketplace. Such access to the clinical market also supports our efforts to penetrate research and pharmaceutical markets.”

“In parallel, our agreement with Bayer is part of our strategy to expand collaborations with drug companies,” stated Page. “The goal is to accelerate and streamline clinical development of new drugs through the identification of important drug response biomarkers.” Other collaborations for Ciphergen include deals with the National Cancer Institute and Johns Hopkins University School of Medicine.

“Additionally,” Page stated, “we have programs overseas. Over 500 of our proteomics chip systems have seeded the research markets in locations all over the world.”

Ciphergen is one of several companies rapidly developing diagnostic capabilities in proteomics. As these efforts mature, pathologists and laboratory directors can expect to see a steady acceleration in the number of proteomics-based assays moving from the R&D pipeline into clinical use.

Proteomics Race Is On

On the positive side, many of these new lab tests will allow for earlier detection of disease, or provide enhanced sensitivity and specificity over existing methods. On the cautious side, it is unclear that most payers will move swiftly to provide coverage for these tests and reimburse them at adequate levels.

Lab managers and pathologists should take note of another dimension of Ciphergen’s business strategy. Its instrument system is designed to be used, with modifications, in both research labs and clinical laboratories. Ciphergen hopes this will compress what has been a rather lengthy period of time between a discovery and relevant research-grade assay to commercialization.

Two Testing Environments

Historically, the research assay is often limited by old platforms—trying to fit the new technology “square peg” to an existing instrument “round hole.” Ciphergen’s strategy is to design a state-of-the-art instrument system which can support the research lab while also performing the high volumes of tests needed by clinical labs.

Because Ciphergen has focused on four types of cancer—breast, ovarian, colon, and prostate—it is likely that the first assays to emerge in the Ciphergen/Quest collaboration will involve these diseases.


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