Scott Patterson Positions Celera for its Next Race: Protein Analysis

AT A GLANCE

Name: Scott Patterson

Position: Vice President, Proteomics, Celera Genomics

Age: 39

Prior Experience: Developed Amgen’s proteomics program,investigator at Cold Spring Harbor Laboratory.

If there is to be a race to identify novel proteins important in disease and medicine, Celera Genomics’ Scott Patterson — the man in charge of Celera’s protein discovery efforts — may have the racing spirit in his blood. As an undergraduate, and later as a graduate student in physiology and pharmacology at the University of Queensland in Brisbane, Australia, Patterson pursued his studies while running an equine blood-typing laboratory for the racehorse-breeding industry.

“Half of the analytical processes that we employed were electrophoretic,” he said. “That’s what really led me into protein analytics.”

Doing graduate work in protein electrophoresis, particularly 2D gel electrophoresis, wasn’t the area of biological research most in vogue at the time — in fact most of his fellow students were interested in becoming molecular biologists. But Patterson wanted to study more than just the latest cloned gene: “I was always interested in the molecules performing the reactions and analysis of those,” he said.

Patterson’s interest in protein function led him to study plasma serine protease inhibitors at the University of Queensland, and then to a faculty position at Cold Spring Harbor Laboratory on Long Island in New York, where he maintained the 2D gel facility and applied protein analysis techniques to his research in apoptosis.

But in 1993, after two and a half years at Cold Spring Harbor, Patterson felt the call of the burgeoning biotechnology industry, and moved to Amgen, in Thousand Oaks, Calif., to continue his research in apoptosis and protein technology development. There, at the urging of his employer, Patterson picked up on early academic work and began pursuing a strategy for using chromatography to separate and identify novel secreted proteins from various biological samples.

“Rather than a 2D gel-based approach, other scientists in academia had shown some limited data on taking a chromatography-based approach, where they were looking at a complex mixture of peptides, and we actually refined that dramatically,” he said. “It was a particularly successful effort.”

The scale of the project, however, wasn’t large enough. Although Patterson wasn’t desperate to leave Amgen, a recruiter from Celera approached him last year, and Patterson couldn’t resist the temptation to escalate his proteomics research. “It was a great opportunity to be able to take this kind of research to a much larger level; it’s really at least an order of magnitude bigger,” he said.

Since joining Celera a year ago, Patterson has spearheaded the company’s foray into proteomics by combining his liquid chromatography-based approach for separating proteins with sister company Applied Biosystems’ (ABI) next-generation mass spectrometry systems, namely, the MALDI TOF-TOF. Celera’s platform relies on commercially available column-packing materials to deplete high-abundance proteins and separate proteins into distinct fractions, before using tryptic digestion to fragment the proteins into smaller peptides. To quantitate differences in protein expression, Celera has applied the ICAT reagent technology, developed by Ruedi Aebersold of the Institute for Systems Biology and licensed by ABI, in tandem with ABI Mariner electrospray TOF and ABI TOF/TOF instruments.

Celera’s acquisition of Axys, and its collaboration with SomaLogic have also played into the hands of Patterson and his proteomics team. Small molecules developed by Axys can serve as useful affinity reagents for certain types of proteins, Patterson said, and SomaLogic’s technology for generating RNA-based aptamers against target proteins can help Celera validate that a target protein is expressed in a specific tissue or serum sample.

Patterson cites the integration of Axys’ technology as evidence of Celera’s focused strategy for identifying only those proteins that have the potential to serve as drug targets. “There are some discovery efforts where we look broadly at differential protein expression,” he said, “but our emphasis is actually on focused discovery.”

Although proteomics has yet to lead directly to a new therapeutic, Patterson believes it’s only a matter of time before Celera comes up with the next blockbuster drug. “We just hope we can be more efficient in our discovery by analyzing at the protein level,” he said. “That’s the bottom line.”

— JSM