Proteomics in 2011 continued its long, hard slog toward the clinic, battling now-familiar challenges like sluggish test sales, unproven platforms, and the vagaries of the regulatory process.
But while clinical proteomics efforts in the past have often been pushed by smallish start-ups, 2011 saw investments in the space from heavy-hitters including Agilent, Myriad Genetics, and Thermo Fisher Scientific.
Whether these companies’ muscle will help proteomics finally fulfill its clinical promise remains to be seen. But in a year filled with difficulties – from large mass spec outfits’ struggles with flatlining government research budgets to small biotech firms’ search for profitable business models – their attentions offered the field a welcome bit of optimism.
Big Names Buy in
Acquisitions played a significant role in the move of some larger firms into the proteomics space, with Myriad kicking things off with its $80 million purchase in April of protein biomarker discovery firm Rules Based Medicine (PM 4/29/2011).
Through the deal, Myriad acquired RBM's biomarker discovery platform as well its pipeline of proprietary protein biomarker-based diagnostics, which includes eight tests currently on the path to commercialization, five of which the company has designated as “high priority” (PM 11/4/2011).
In September, Myriad added to its proteomics portfolio with a $25 million debt investment in molecular diagnostic firm Crescendo Bioscience that included a three-year option to purchase the company (GWDN 9/9/2011). Crescendo specializes in tests for autoimmune and inflammatory diseases like rheumatoid arthritis. Its first product is Vectra DA, a laboratory-developed test that measures levels of 12 proteins in blood to assess rheumatoid arthritis activity.
Thermo Fisher likewise made a clinical proteomics buy, acquiring in September Intrinsic Bioprobes, a protein biomarker firm founded by Arizona State University Biodesign Institute researcher Randall Nelson (PM 9/2/2011). The company, which had in the past collaborated with Thermo Fisher on several protein biomarker projects, specialized in immunoenrichment-based sample prep tools for mass spec-based biomarker workflows and for quantitating levels of different protein isoforms.
In April, prior to the acquisition, IBI launched its first in vitro diagnostic, an IVD for kidney disease and renal failure comprising assays for beta-2-microglobulin, cystatin C, and retinol binding protein. That test is currently available through the CLIA-certified laboratory at the University of Medicine and Dentistry of New Jersey's Institute of Genomics Medicine.
In an interview following the acquisition, James LaDine, global director of research and development for Thermo Fisher's Lab Consumables Division, told ProteoMonitor that the company would use the acquisition to expand its reagent offerings for clinical proteomics customers, as well as to accelerate its own in-house assay development program (PM 9/23/2011).
Thermo Fisher has a "substantial" list of clinically relevant analytes it has identified for assay development, he said, and is "working down the list" using IBI's mass spectrometric immunoassay, or MSIA, technology. He declined to say what analyte the company would focus on first or when it hoped to bring a test to market, but, he said, “we know what [the analyte] is, and we understand its performance pretty well."
Agilent made a move with its buy of Biocius Life Sciences, developer of the RapidFire high-throughput separations platform that could prove key to the company’s clinical proteomics ambitions (PM 3/4/2011).
More than acquisitions, though, Agilent’s investment in the field revolved around its collaboration with Leigh Anderson on an automated workflow for his stable isotope standards and capture by anti-peptide antibodies, or SISCAPA, assay. Anderson is CEO of SISCAPA Assay Technologies, a company formed to commercialize the method.
An immunoaffinity-based mass spec assay that combines antibody-based peptide enrichment with mass spec, SISCAPA is a potentially significant technology for clinical proteomics as it could provide a sensitive, reproducible, high-throughput workflow for biomarker validation or clinical work requiring analysis of hundreds or thousands of samples.
Key to establishing the workflow as a clinical tool is moving it to an automated platform, an effort on which Anderson and Agilent have been collaborating. At the Association for Mass Spectrometry's Applications to the Clinical Lab meeting in February, Anderson presented an automated SISCAPA workflow using an Agilent Bravo liquid handling system for sample prep attached to an Agilent 1200 series LC system and an Agilent 6490 triple quadrupole instrument (PM 2/11/2011).
At the American Society for Mass Spectrometry annual meeting in June, Gustavo Salem, vice president and general manager of Agilent's Biological Systems division, told ProteoMonitor that the company was "actively in discussion about ways to bring the technology both to a set of pharma clients as well as to the clinical vision [Anderson] has always talked about where this becomes a set of reagents for clinical diagnostics."
Potential and Pitfalls for Mass Spec
Thermo Fisher and Agilent’s efforts notwithstanding, the first company to push mass spec-based proteomics into the clinic could be Salt Lake City, Utah-based Sera Prognostics, which plans to launch a mass-spec protein biomarker preterm birth diagnostic in the first half of 2013 (PM 11/18/2011). Such a product would mark one of the most ambitious clinical efforts to date for mass spec-based proteomics.
In November, the company closed a $19.3 million Series A financing round and appointed former Myriad Genetics president Gregory Critchfield as its new CEO. In an interview following his appointment, Critchfield told ProteoMonitor that, while previous work on the test – which measures levels of three proprietary peptides plus six additional proteins to predict preterm birth in pregnant women – had been done via both mass spec and immunoassay, the company had since decided to move it entirely to a mass spec platform.
This development is obviously encouraging for mass spec vendors, but using mass spec as a platform for clinical proteomics comes with potential complications, as well.
Specifically, vendors looking to use their instruments for clinical testing could find those instruments subject to increased regulation from the US Food and Drug Administration. Mass spectrometers are exempt from FDA’s 510(k) approval process, but, noted Mya Thomae, CEO of IVD regulatory consulting firm Myraqa, they still would need to be registered under the agency’s quality systems regulation to be used for clinical proteomics tests.
Although such registration is a straightforward process, it requires documentation of any upgrades or changes to the equipment. This, Thomae told ProteoMonitor, could make mass spec vendors reluctant to register their instruments, particularly given the pace of advancement in the field.
“If you’re not under the quality systems regulation, you have a lot more flexibility in terms of upgrading your instrument, changing things around, and not needing the same level of documentation,” she said. “So, particularly for technologies that are moving quickly, the [research-use-only] environment allows [firms] a lot more flexibility.”
Thomae also suggested that, as 510(k)-cleared proteomic diagnostics come onto the market, FDA could require vendors to take the platforms running those tests through the 510(k) process, as well.
“FDA likes to look at things as systems, so [if] we had a Class II [510(k)-cleared] assay, would FDA want to see a [510(k)] submission on the instrument to go along with that assay?” she said. “So you may be able to enter the market as a [510(k)] exempt product, but then as you put more sophisticated assays on it, FDA [requires a 510(k)] because you’re part of a Class II system.”
In an October conversation, Agilent applications solution manager Keith Waddell acknowledged this possibility, telling ProteoMonitor that FDA is “starting to consider mass spectrometry more and more now as an IVD system, and therefore their aim is for us to generate 510(k) submissions [that] would include clinical data to verify that the system works in a clinical environment.”
He said that for most mass spec vendors, such requirements are “a little premature” and have led to cautiousness about “stating that we have products for the clinic.”
“Obviously the long-term vision that most of us [mass spec] vendors have is to end up with clinical devices,” Waddell added, “but there’s a process that you have to go through.”
Diagnostics Struggle, Mass Spec Slumps
Part of that process, of course, is developing and marketing clinical tests, and here, as in years past, proteomics firms had their share of difficulties.
Notably, bankrupt diagnostics firm Correlogic completed its long demise, selling its assets at the beginning of December to fellow ovarian cancer testing outfit Vermillion for $435,000 in cash.
Vermillion suffered its own woes. While the company sold more than 12,000 OVA1 tests in 2011 – roughly double the number it sold in 2010 – this was still well short of the 65,000 to 80,000 tests per year it would need to break even given its current spend rate.
Furthermore, the amount of revenue that will ultimately be recognized from these sales was called into question as Vermillion shareholder George Bessenyei alleged that Medicare has been denying OVA1 claims at a rate of more than 80 percent. If true, this could significantly lower the revenues expected from the OVA1 tests Vermillion has reported as performed in its 2011 earnings reports (PM 12/23/2011).
This week, Vermillion said it would be restructuring in 2012 “to reduce headcount and other expenses” and announced the resignation of chief financial officer Ashish Kohli, who left due to the elimination of his position, the company said. It also reduced its board from eight to seven members and eliminated four territory development managers and one regional sales director role (see story this issue).
The mass spec industry also saw restructuring with Thermo Fisher announcing in November that it had cut 890 jobs since the start of 2011 (GWDN 11/4/2011).
Like many mass spec vendors, Thermo Fisher suffered from weakness in the US government and academic markets. In October, the company lowered its full-year 2011 guidance based on weak demand for research products including mass spectrometers and liquid chromatography systems (PM 10/28/2011). Waters also lowered its 2011 guidance, citing declines in academic spending (PM 10/28/2011).
During Bruker's Q3 earnings call, president and CEO Frank Laukien similarly noted "weakness in US academic spending" (PM 10/28/2011); as did Agilent during its Q4 2011 call in November (PM 11/18/2011). Nick Roelofs, president of Agilent's Life Sciences division, said the company expects this trend to continue into 2012, noting that the National Science Foundation's budget for 2012 will be down roughly 2.4 percent and the National Institutes of Health budget will be only slightly up.
Top-Down, Bottom-Up Breakthroughs
Commercial concerns aside, proteomics reached several research milestones in 2011, most notably the emergence of high-throughput top-down proteomics as a team of scientists led by Northwestern University researcher Neil Kelleher used a new top-down workflow to identify more than 3,000 protein species in an analysis of HeLa S3 cells (PM 11/4/2011).
Bottom-up, peptide-based proteomics has dominated the field for the last decade, but interest in top-down methods has grown as improvements in instrumentation have made analysis of intact proteins easier and researchers have become increasingly aware of the importance of protein isoforms and post-translational modifications.
Top-down research has remained relatively low-throughput, however — a limitation Kelleher’s work will help remedy.
As noted by Princeton researcher Ben Garcia, whose lab also focuses on top-down work, the study, which was published in Nature in November, marked a 20- to 30-fold increase over previous top-down MS results. Andreas Huhmer, proteomics marketing director at Thermo Fisher Scientific, compared Kelleher’s research to Scripps scientist John Yates’ groundbreaking 2001 work demonstrating the feasibility of high-throughput bottom-up proteomics.
Such bottom-up techniques closed in on a milestone last year, as well, as a trio of research teams approached what appeared to be the outer limits of conventional LC-MS-based human proteome analysis.
In three separate papers, the labs of Utrecht University researcher Albert Heck (PM 12/2/2011), Swiss Federal Institute of Technology Zurich scientist Ruedi Aebersold (PM 11/18/2011), and Max Planck Institute researcher Matthias Mann essentially saturated the human proteome accessible via the LC-MS/MS workflow that they used, with each group identifying more than 10,000 proteins.
“We see in our analysis that you don’t get more [protein] identifications by reanalyzing the samples,” Javier Munoz, a postdoctoral researcher in Heck’s group, told ProteoMonitor in an interview following publication of their work.
”It’s interesting that the three studies published at almost the same time, using pretty much the same technique, ended up with more or less the same number of proteins,” he said.
Both Aebersold and Munoz noted that use of different sample-prep techniques and different enzymes to create peptide digests would likely enable access to additional proteins, but, Munoz said, “I think we are pretty close to full proteome coverage. I think we could maybe start to say that this is the number that reflects the total protein content of human cell lines.”
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