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Target Discovery Working With MD Anderson, EVMS to Develop Isoform-Based Cancer Dxs

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Two years after completing proof-of-concept experiments for its IDBEST technology, Target Discovery has formed collaborations with the MD Anderson Cancer Center and the Eastern Virginia Medical School to develop protein isoform-based diagnostics for breast, prostate and ovarian cancer.

The Palo Alto, Calif.-based company is currently picking a list of biomarkers that will be examined for isoform differences. Researchers will then whittle down the markers to two or three promising isoforms on which to perform a larger validation study.

After validation, Target Discovery plans to develop an "isonostic assay" based on its capillary electrophoresis platform, and to conduct a blinded study of about 80 disease and 80 control samples. If the study goes well, the company then hopes to move the assay into clinical laboratories via the CLIA route.

"The base timeline is that within about two years, we expect to have our first isonostic assay on the market," said Target Discovery CEO Jeffrey Peterson. "Within a four-year period, we anticipate having three assays in market."

The collaboration with MD Anderson, announced two weeks ago, will initially focus on breast cancer, and then ovarian cancer, while the collaboration with EVMS, announced in March, will focus on prostate cancer.

"MD Anderson will bring the clinical samples and the longitudinal patient histories to the collaboration," said Peterson. "Obviously, they have a tremendous knowledge of the disease and the clinical side of things."


"The base timeline is that within about two years, we expect to have our first isonostic assay on the market."

At EVMS, Target Discovery will be collaborating mainly with Oliver John Semmes' research group and the Virginia Prostate Center.

"We're in the early stages of developing the clinical protocols," said Peterson.

Target Discovery developed its Isotope-Differentiated Binding Energy Shift Tags, or IDBEST, technology as a hypothesis-driven approach that deviates from traditional global proteomics, and instead hones in on finding isoforms of proteins that are specific for a disease.

"You see instances of specific isoforms correlating with disease or drug response all over the place," said Peterson. "The poster-child example is prostate specific antigen. The painful truth with PSA is that about 75 percent of the time, it gives a false positive result. Well, there are multiple isoforms of PSA, and one correlates to prostate cancer, but a traditional immunodiagnostic assay can't distinguish between isoforms, so that has impacted on the specificity of the assay."

Instead of looking at global proteomes for biomarkers, Target Discovery starts with a list of potential biomarkers that have been linked to a disease. It uses antibodies to pull those biomarkers out of the global proteome, then uses IDBEST to look at quantitative expression differences between isoforms in diseased and control samples.

IDBEST is based on a subnuclear physical property, Peterson explained.

"When you form the nucleus of an element, there's a release of energy called the nuclear binding energy, and [thereby] a loss of mass, called the mass defect," he said. "All of the elements involved in a biomolecule have a very similar mass defect shift. However, there are elements such as bromine or iodine that have a greater mass shift. We incorporate bromine and/or iodine into the [protein] tag, and then we can pull out the molecules whose [mass defect] phase is shifted by one-tenth of a mass unit."

The IDBEST technology allows proteins of interest to be pulled out from a large background of other proteins directly after the capture antibody step, Peterson said.

"After the proteins have been captured by the capture antibodies, you've still got quite a gemisch of proteins," he said. "With IDBEST, you can avoid the simplification step that would be needed using a global proteomic technique, and use the mass defect to pull out a family of proteins of interest from the massive background."

Once an isoform or group of isoforms has been correlated to a disease state, researchers plan to validate them on a larger group of samples. If the validation studies go well, researchers then plan to develop a diagnostic test using Target Discovery's proprietary capillary electrophoresis technology.

"We made a seminal breakthrough in capillary electrophoresis technology in that we designed a line of dynamic [capillary] coatings that allow us to set the electroosmotic force wherever we need it," Peterson explained. "We've been able to grab the controls for CE separations, and that allows us to optimize separation conditions for difficult separations. For example, with bovine serum albumin, there are three different isoforms that don't even have mass differences. We're able to pull them apart like three fingers on your hand."

There are a number of companies competing within the proteomic molecular diagnostics space, but Target Discovery has a fairly unique position in terms of having the technology to identify and develop diagnostic isoforms, or isonostics, Peterson said.

"Companies like Ciphergen and Intrinsic Bioprobes are working within the proteomic area, and grappling with some of the same issues regarding isoforms, but I don't see anyone positioned with a technology set like ours," he said.

In addition to its current cancer research collaborations, Target Discovery is also looking to form more partnerships, possibly for different disease areas such as Alzheimer's disease and blood-clotting diseases, Peterson said.

— Tien-Shun Lee ([email protected])