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Applied Proteomics Snags $22.5M in Funding; Aims to Optimize Mass Spec-Based Biomarker Discovery


By Adam Bonislawski

Protein biomarker firm Applied Proteomics said this week that it has raised $22.5 million in a Series B financing round, moved its corporate headquarters to San Diego, and appointed as CEO former Predictive Biosciences CEO Peter Klemm.

The company will use the funding to identify diagnostically useful protein biomarkers via its mass spec-based discovery platform, with an initial focus on markers for oncology, cardiology, and emergency room care, Klemm told ProteoMonitor.

Domain Associates, Vulcan Capital, and returning angel investors provided the funding, which follows an initial $4 million angel investment that launched the company in May 2007. Concurrent with the Series B round, the company has added James Blair, a founding partner at Domain, to its board of directors.

Since its founding in 2007 by David Agus, director of the University of Southern California's Center for Applied Molecular Medicine, and Danny Hillis, chairman and co-founder of technology firm Applied Minds, API has flown largely under the radar.

This quiet approach, said John Blume, API's chief scientific officer, was in part due to the company's focus on first fine-tuning its platform before jumping wholeheartedly into discovery work — a strategy, he told ProteoMonitor, that it hopes will help it avoid some of the frustrations that have stymied other protein biomarker discovery outfits.

"I think we set ourselves a pretty high standard, saying that the reason that proteomics approaches to biomarker discovery have failed before is that people just went out and bought the latest cool and groovy technology and then tried to apply it to a biological problem," he said.

Indeed, as efforts to move protein biomarkers into the clinic continue to flounder, a number of researchers have suggested that rather than invest further in proteomics-based discovery efforts, the field would do better to concentrate on validation and clinical implementation of previously identified markers.

For instance, at the Association for Mass Spectrometry's fourth annual Applications to the Clinical Lab meeting last month, Swiss Federal Institute of Technology Zurich researcher Ruedi Aebersold suggested in a lecture that because "it has been enormously difficult for many laboratories to collect hundreds of samples of cohorts from healthy and disease-affected individuals, and to do very thorough plasma proteomic analyses … it's reasonable to assume that increasingly biomarker candidates will come from genomics and bioinformatics rather than from comparative proteomics ... [and that] the objective of proteomics in biomarker research will shift from discovery to validation" (PM 1/20/2012).

In an interview with ProteoMonitor last month, Stanford researcher Tony Wyss-Coray likewise noted that limited sample sizes have confounded protein biomarker discovery efforts, and suggested that comparison of not hundreds, but thousands of samples is needed to account for technical and biological variability (PM 12/30/2012).

API hopes to overcome these difficulties, Blume said, by significantly reducing the technical noise associated with mass spec-based discovery.

"What [Agus and Hillis] said was let's put [the mass spec platform] together in a way that's more like a semiconductor manufacturing process-level attention to detail than just your average post-doc who has a brand new mass spec," he said. "The differentiating factor for us is that we've got the thing humming so well that we've effectively dialed the noise component way down, and that gives us tremendous reproducibility, and that translates into very practically sized studies."

Blume said that the company "typically runs studies with arms of 50 or so, and we get very good power to see the actual underlying biological signal."

Adair Newhall, an associate with Domain Associates, said the precision of API's platform was a key driver of his firm's interest in the company, noting that "they are able to really get rid of the noise that comes with some of the other [mass spec] systems that have been used."

Both Blume and Adair declined to say what, specifically, about the platform enabled the decrease in noise. Although the company is not aligned with any particular vendor, it has done the bulk of its work thus far on Agilent Q-TOF instruments, which, Blume said, provided the combination of qualitative and quantitative measurement they were looking for.

Blume added that the company was in the process of adding instrumentation, although he didn't give particulars.

The company's platform is aimed at the discovery and early validation stages, Blume said, noting that it will most likely move markers that emerge from the system "to some other more practical and efficient test format" like an immunoassay.

He added, though, that "we're very enamored of the idea [of] the coming wave of deployment of mass spec in clinical laboratories."

API's immediate focus, Klemm said, is identifying markers that could prove useful within current treatment paradigms. For instance, with regard to the firm's oncology ambitions, he cited the example of biomarkers that could better determine which patients should be moved on to invasive procedures like colonoscopies and biopsies.

In the cardiology space, the company is investigating biomarkers that could prove useful in detecting coronary calcification, which is typically done via CT scans.

"The key for us is being in the flow of medical paradigms," Klemm said. "We don't necessarily want to replace existing paradigms — just make them simpler, faster, and more accurate. [We] want to be on the right side of the healthcare equation in that you want to save healthcare costs by not spending it on the patient that doesn't necessarily need it."

He added that, while the company's main focus is the development of proprietary protein-based diagnostics, it would also consider partnering with pharma on companion diagnostic work. He noted, however, that it had no interest in using its platform for basic fee-for-service work.

API doesn't currently have a timeline for commercialization of any of the diagnostics it is working on, Klemm said, noting that the company is "building its portfolio" and expects to "have over the next few years projects in various stages of either commercialization, late-stage development, or discovery."

The firm currently has 16 employees and plans to grow that number to around 25 over the course of this year, he said.

Have topics you'd like to see covered in ProteoMonitor? Contact the editor at abonislawski [at] genomeweb [.] com.