By Kevin Davies
October 10, 2012 | As biotech catchphrases go, “personalized proteomics” hasn’t quite registered as much as some, but according to Swiss biotech company Biognosys, recent advances in mass spectrometry and bioinformatics could have enormous ramifications for biomedical research, drug discovery, and even consumer health.
“We have the tools and technology to measure in principal every protein in every sample from every organism,” says co-founder Philipp Antoni. “Can we move personalized genomics into the proteomics field?”
Based in Zurich, Biognosys was co-founded out of Ruedi Aebersold’s research lab at the ETH Zürich in 2008. Aebersold is a noted proteomics researcher who also co-founded the Institute for Systems Biology in Seattle together with Leroy Hood before returning to his native Switzerland. Besides Aebersold, Antoni, Johan Malmstroem and Oliver Rinner form the core team of Biognosys. Michael Sidler (of Swiss VC company Redalpine) joined the company early on as a coach and investor.
After stealthily growing the technology over the past few years, with several pharma customers such as Novartis and Pfizer in the fold, as well as Philips, Sidler says Biognosys’ technology is ready to take the next step, touting its reliability and multiplexing capability.
“We can quantify thousands of proteins within hours from basically any type of sample,” says Sidler, “even whole proteome measurements of model organisms. The potential for Biognosys’ technology is very broad. Biomarker development is really just the beginning. The patient and personalizing diagnostics and treatment is our goal. Now it’s time to go to the US, which is a couple of years ahead of Europe in personalized medicine.”
Synthetic proteomes enable the development of a specific assay for each protein. By predicting the protein sequence and the peptides released by enzymatic cleavage, matching (step 1-3) synthetic versions of the target peptides are synthesized (4). Several hundreds of these synthetic peptides are analyzed in parallel in a mass spectrometer. The data generated (5) provides pure signals that consitute a fingerprint of each protein (7). This synthetic fingerprint provides a highly specific template for matching signals from blood or tissue.
Antoni argues that Biognosys’ targeted proteomics technology overcomes previous issues facing the industry. “Before you measure a particular protein in a particular sample, we need to determine and validate the assays—the protein’s specific fingerprint—and then run the real samples,” he says. Biognosys has developed proprietary algorithms and a software workflow that can specifically measure the abundance of potentially every protein in a highly multiplexed fashion. Antoni says that Biognosys routinely measures hundreds of targets in a single experiment, and entire proteomes are within reach.
Biognosys has built a library of some 80,000 assays covering the entire human proteome, providing 3-4 unique peptide fingerprints on average for every protein. Proteomes of other organisms are also being developed. Customers can buy the assays to perform research at their site or just rely on Biognosys to conduct their measurements.
Many biomarker companies, including Larry Gold’s SomaLogic in Colorado, are devising methods to identify and quantify proteins in the blood—what Sidler calls “the mirror of health.” The goal is to measure not just subsets of proteins or single proteins, but to provide a real-time readout on health and disease status. In a recent paper in Science Translational Medicine (Huttenhain R. et al. Sci Trans Med 11 July, 2012) applying Biognosys` technology blood and urine samples from cancer patients were screened for potential biomarkers applying targeted proteomics.
“Personalized proteomics could measure every disease state at once. We believe we need panels of biomarkers, not just single biomarkers for each disease,” says Sidler.
This is a technically challenging task, to say the least. The levels of protein biomarkers in blood vary dramatically within and between people, while levels of the same protein in the same person can vary dramatically day to day. There are orders of magnitude differences in the concentrations of different proteins in the blood. “This comparison of individual protein concentration levels against the population average is one reason it’s so difficult to find good biomarkers,” says Antoni.
Other companies have tried to commercialize proteomics but with mixed results. Biognosys hopes to avoid the fate of GeneProt, a company co-founded a decade ago by noted proteomics researcher Denis Hochstrasser. GeneProt had a similar vision using “shotgun proteomics, many mass spec machines and a lot of IT,” says Sidler. The company closed its doors in 2005.
Biognosys is developing and deploying two new proteomics technologies—Multiple Reaction Monitoring (MRM), which measures hundreds of proteins in a single assay—and Hyper-RM (or “SWATH” technology), which has the potential to measure an entire proteome in a single run, and was co-developed by Aebersold and Biognosys (see Gillet L.C. et al. Molec. Cell. Proteomics Jan 18, 2012).
Each protein in a sample is identified via a peptide ‘fingerprint’—typically 2-5 peptides per protein. The mass and charge of each constituent prototypic peptide provides a unique identifier for each of the several thousand proteins present in blood (or practically any other source). Biognosys has filed several patents covering its protein assessment technology and the corresponding data analysis. In addition to various diagnostic applications, biomarker panels can be certified by FDA as tools for clinical trials.
Of the two technologies under development, it is the potential of the SWATH platform that company insiders are most excited about. SWATH is made possible by improvements in instrumentation, particularly new mass spec platforms such as the TripleTOF 5600 from ABI-SciEx. The platform was announced earlier this year and should be commercially released by the end of 2012.
Sidler says, “The real challenge that Biognosys solved is the bioinformatics. Our know-how to determine the unique mass-fingerprints, to filter the signals and to do everything in a highly multiplexed fashion, are the key ingredients.”
Blood contains around 3,000 proteins out of the 20,000 encoded in the human genome. “Blood is very special,” he says. “Just 10 proteins make up 90% of the total protein mass.” To quantify proteins accurately, sample preparation techniques are crucial. “It has to be simple enough to allow large-scale deployment but the unique composition of each sample has to be preserved,” he says. “It took us some time and effort to figure out the parameters. Now with years of experience with all sorts of matrices, from bacteria to yeast and even plant tissue, human plasma is actually not the worst type of matrix.”
The SWATH method enables Biognosys to generate a proteome map in a single run in about two hours. The highly abundant proteins can be depleted or left intact, depending on the question being asked. Thanks to the fingerprint database, the Biognosys software reveals the identity of every peak using pattern recognition software. As with next-gen sequencing, in next-gen proteomics, bacteria served as proof of principle. Studies on bacterial proteomes show that it is possible to cover the full proteome of an organism, as described in several scientific publications (see, for example, Malmström et al. Nature 460, 762-765, 2009).
By spiking the samples with peptides laced with heavy atoms such as C13 or N15, it is possible to quantitate the levels of peptides in the sample. “We have developed software to do fully automated analysis, providing an objective readout of the data—no human error,” says Antoni.
Although still some way off, Biognosys executives don’t shy away from predicting a time when it will be possible to produce personalized proteomics maps that could be analyzed at regular intervals, for example during annual physical exams. “Then you can store all that information in a digital biobank to determine your personal baseline,” says Sidler. From there, it would be possible to perform retrospective analyses, dipping back into the consumer’s digital proteomic history, explore post-translational modifications, and more.
The Biognosys brain trust believes there is value in complementing genomics with proteomics. “We can measure a lot of proteins—we’d include the genes and correlate with our own data—to get a more complete picture of the health of the person,” says Antoni.
“If I [were in] a personal genomics company, I’d die for this technology,” says Sidler. “I could test my customers every year. It’s great to know your genomic profile/risk, but your protein profile will tell you how you’re doing right now.”
It is only a matter of time, Sidler thinks, before proteomics tests reach the doctor’s office. “Knowing your body’s state and picking up problems as early as possible is our goal, long before symptoms occur or your physician would order a regular test.”