Applied Proteomics, Co-Founded by Danny Hillis, Gets New CEO, $22.5M

2/7/12Follow @bvbigelow

Applied Proteomics hasn’t exactly been operating in stealth mode since it was founded five years ago. Co-founders David Agus, a cancer specialist at USC, and Danny Hillis, the MIT-trained computer scientist, gave TedMed talks about the startup’s technology, which provides a 40-gigabyte snapshot of all the proteins circulating in a drop of blood. By pure coincidence, I watched John Stewart’s Feb. 2 interview with Agus last night on “The Daily Show.”

“Danny and David had the foresight to build the tool before trying to use the tool,” says John Blume, a molecular biologist who joined API in 2008 as chief scientific officer. “Although the company wasn’t in stealth mode, the first several years were spent in taking the time to make it right, and then to use it and avoid some of the stumbling blocks.”

Now Applied Proteomics is raising the curtain on several steps that mark its progress beyond a seed-stage startup that was incubating at Applied Minds, an industrial think tank that Hillis founded in Glendale, CA, with a colleague from Disney Imagineering. After moving the headquarters to San Diego late last year, Applied Proteomics is today naming a new CEO—Peter Klemm, a veteran in molecular diagnostics and the former CEO of Lexington, MA-based Predictive Biosciences.

Danny Hillis

The company known as API says it also secured $22.5 million last June in Series B funding from Domain Associates (San Diego partner Jim Blair joined the board), Seattle’s Vulcan Capital, and returning angel investors. Klemm tells me the company raised $4 million from angel investors (who prefer to go unnamed) in what amounted to API’s Series A round in 2007.

David Agus

API’s goal, Klemm says, is nothing less than to “elevate molecular diagnostics to another level beyond the genome” by measuring the proteins made by genes—a long-sought technology that is expected to help doctors improve medical care for individual patients. Because proteins carry out most cellular functions, the company says a snapshot of all the proteins circulating in the body at a given moment represents “the most powerful source of information” in terms of understanding a patient’s health status.

Quantifying all the proteins in the body, Klemm says, can help doctors optimize the course of treatment for individual patients by making it easier to identify the specific drugs that would have the greatest effect on blocking specific proteins or signaling pathways, which can vary dramatically from person to person.

In a statement from the company, Hillis says, “For the first time, we can look at all the proteins in the body with remarkable specificity and sensitivity and use proteomic technology to create superior diagnostics that can ‘listen to the conversation of the body.’”

Where genome sequencing provides detailed information about the genes that make up each individual, Blume and Klemm says proteomics (the study of proteins) takes molecular diagnostics to a new level by describing what the genes are actually doing. In his 2010 TedMed talk, Hillis compared genome sequencing to listing all the ingredients a particular restaurant could use to prepare meals. Quantifying the proteins helps to explain what’s actually happening in the kitchen—how the ingredients are being used and what meals are being made.

John Blume

While scientists have gotten very good at generating information about proteins, Blume says it was necessary to take a systems level approach to accurately measure all the proteins in a blood sample, and then use that data in a meaningful way. “Molecular medicine is now as much about information handling as it is about measurements,” he says.

In API’s statement, Agus says the company “has significantly advanced the technology to look at the whole proteome instead of a single protein biomarker and have a complete picture of a patient’s status to make the best healthcare decisions.”

API has been hiring since it moved to San Diego, and Klemm said he expects the company will reach 25 employees sometime later this year. They will be focused primarily on discovery and development work.

Klemm says he has extensive experience in developing markets for high-value diagnostic tests. Before joining Predictive Biosciences, Klem was the CEO of San Diego’s GeneOhm Sciences, which he joined in 2002. Becton Dickinson acquired GeneOhm in 2006 for roughly $255 million. Klemm also currently serves as chairman of Pathwork Diagnostics, a Redwood City, CA, company that specializes in cancer diagnostics.

Bruce V. Bigelow is the editor of Xconomy San Diego. You can e-mail him at bbigelow@xconomy.com or call (619) 669-8788 Follow @bvbigelow

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