Applied Proteomics Snags $28M to Look for Disease Markers in Blood

Xconomy San Diego — 

San Diego’s Applied Proteomics, founded in 2007 to automate the process of accurately measuring all the protein fragments in a drop of blood, has raised $28 million in a Series C round of financing.

With the addition of the latest round of financing, Applied Proteomics has now raised a total of $57 million over the past six years, according to CEO Peter Klemm. The Malaysian conglomerate Genting Berhad led the latest round, and was joined by existing investors Domain Associates and Vulcan Capital, the investment vehicle of billionaire Paul Allen.

The company plans to use the proceeds to commercialize its diagnostics technology, which offers near-term use in early cancer detection and long-term potential as a method for monitoring a patient’s systemic health at a fundamental level. Applied Proteomics’ plans include construction of a clinical laboratory in San Diego to house advanced, high-throughput mass spectrometry assays.

As part of its commercialization strategy, Applied Proteomics plans to develop a blood test for specific protein fragments that are thought to be the precursors of colorectal cancer. Under the company’s business plan, patient blood samples would be sent to the lab for testing. Results would be returned to a patient’s physician in two to three days.

The test is not intended to replace the colonoscopy, the current standard of care, according to John Blume, Applied Proteomics’ chief scientific officer. But the procedure is invasive and its costs can run high and vary from place to place. About half of the Americans who are encouraged to have a colonoscopy—about 44 million—avoid the procedure, Blume said in a telephone interview. Yet early detection through colonoscopy makes colon cancer one of the few cancers that is preventable. So the blood test would be offered as a way to screen patients who choose not to undergo a colonoscopy, Blume said.

The technology being developed by Applied Proteomics would take diagnostics to an unprecedented level of detail, by detecting the aberrant proteins (and protein fragments) produced by mutated and malfunctioning genes. As Klemm puts it, “We have the potential to dramatically reduce the incidence of colon cancer, which currently claims 50,000 lives per year in the U.S. alone.”

Applied Proteomics intends to eventually provide a much bigger picture—a 40-gigabyte snapshot of all the protein fragments circulating in a drop of blood. It is an ambitious goal. The roughly 25,000 genes that make us human give rise to hundreds of thousands of different proteins—the complete proteome. Because proteins carry out most cellular functions, a snapshot of all the proteins circulating in the body would amount to a systemic measurement of a patient’s overall health.

Charting the proteome over time—and tracking the changes in more than 300,000 specific protein biomarkers—would create an even more powerful diagnostic tool by detecting the early signs of disease before they play out. The highly specific nature of the company’s diagnostics would enable healthcare providers to prescribe precise treatments for patients before symptoms appear.

This is the vision that USC cancer specialist David Agus and the renowned computer scientist Danny Hillis had in founding Applied Proteomics.

While the company pursues that ambitious long-term goal, Klemm and Blume said that in the near-term they plan to develop diagnostic tests for another 20 or 30 specific diseases, which would both demonstrate the power of the technology and generate more immediate revenue for the company.

In a statement from the company, Hillis said, “This investment validates our vision for API and signifies that the investor community is ready to commit to transforming healthcare.”