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Quanterix Snares $185K SBIR Grant to Develop Way to ID Hard-to-Find Proteins

Quanterix is developing a technology aimed at allowing researchers to detect low-abundance proteins, and last week announced it had received its first federal grant to continue developing the platform.
The Cambridge, Mass., company will use the $185,000 Phase I Small Business Innovation Research grant from the National Cancer Institute to apply its assay-based technology, called Single Molecule Array, or SiMoA, to detect prostate cancer, company chairman and CEO Nicholas Naclerio told ProteoMonitor last week.

”When you come in with a 100- or a 1,000-time improvement in performance, people will pay attention.”

While the underpinning technology behind SiMoA is based on the standard Enzyme-Linked ImmunoSorbent Assay, it takes the ELISA technology further by digging deeper into a sample to mine for more details by dividing the sample into many smaller sub-samples, and then performing an ELISA on each sub-sample.
According to Quanterix’s website, SiMoA uses arrays of femtoliter-sized reaction vessels, each holding a single molecule of interest. The arrays consist of up to hundreds of thousands of such reaction vessels etched into the end of an optical fiber bundle.
“Each reaction vessel is isolated from neighboring vessels and, when incubated with dilute solutions, can be used to trap single molecules according to Poisson statistics,” the company said. 
Each vessel containing an individual molecule is interrogated via a set of proprietary assay chemistries and an optical detection system. The optical fiber bundle carries light into and out of each reaction vessel, in effect making each well an independent assay for each single molecule.
Using a proprietary instrument comprising a light source, optics, digital camera, and automated handling system, the tool detects molecules and uses software to analyze images to determine the behavior of individual molecules.
While ELISAs are based on “fundamentally an analog technology” that generates a fluorescent signal that is proportional to the concentration of the analyte being measured, Quanterix has “turned that into a digital technology,” Naclerio said.
For each individual molecule isolated in a reaction vessel, “We ask the question, ‘Is there one or more molecule present?’ And that way we can very precisely count up how many molecules are present in the sample and get a very precise and very sensitive answer,” Naclerio said.
SiMoA has a sensitivity that is “several orders of magnitude” greater than a traditional ELISA, he added, allowing the platform to detect things at “much lower levels. It means we can detect faster, it means that we can detect it at smaller sample volumes.”
The technology, he said, would help researchers in an area of growing interest in proteomics and protein analysis: low-abundance proteins. In serum, especially, interest is intensifying to get to such proteins because they may prove to be the most promising disease biomarkers.
However, because of a dynamic range that runs at least 10 orders of magnitude, detecting low-abundance proteins in blood has proven to be especially elusive. In blood, the 10 most abundant proteins account for 90 percent of all proteins found, obscuring the lower-concentration proteins from detection.
The field is not short on possible solutions, however. In addition to commercially available products such as columns and chemistries that vendors say remove the most abundant proteins or amplify low-abundance ones, researchers are developing new techniques to deal with low-abundance proteins.
And this summer a new company, Ceres, was launched seeking to capitalize on technology developed by Lance Liotta and Emanuel Petricoin seeking to capture low-abundance proteins and prevent their degradation [See PM 07/24/08].
Still, nothing indicates that a consensus solution has been found.
But according to Naclerio, the sensitivity achieved by SiMoA is about 1,000-fold greater than with a conventional ELISA. In addition, he added, the increase in sensitivity comes without a loss in specificity.
“This method is able to pick out the rare molecule in the background of the very high-abundance molecules,” he said. “We’re talking about things that are 12 to even 15 logs down in concentration from the highest abundance proteins in serum.
“It’s measuring things that are in low-abundance or measuring things that are, for example, high abundance in one place, like in a tumor, but low abundance in another place, like your circulating blood supply,” he said.
Because SiMoA is a general platform, it can also be used for small molecules and nucleic acids, said David Duffy, senior director of platform technology for Quanterix, who also is the principal investigator on the SBIR grant.
Quanterix will use the 18-month grant to prove the utility of the technology at identifying cancer biomarkers, particularly prostate cancer biomarkers. According to the grant abstract, to lower the limit of detection of SiMoA, “surface chemistries will be developed to minimize or eliminate non-specific binding of biological molecules from a complex matrix such as human serum.” The chemistries will incorporate immobilized antibodies to capture and detect low-abundance proteins.
In addition, the firm will use the grant to implement the new surface chemistries to develop a “high-sensitivity assay for prostate-specific antigen.”
Quanterix was founded in the spring of 2007 by Naclerio and David Walt, a professor of chemistry at Tufts University, whose laboratory developed the SiMoA technology. Walt is also the scientific founder of Illumina.
Quanterix’s main backers are venture capital firms Arch Venture Partners, Bain Capital Ventures, and Flagship Ventures. In August, the firm closed the second tranche on a Series A financing, raising about $15 million in total. In November, Quanterix set up its laboratory.
Quanterix chose to detect proteins in serum for the first application of SiMoA because “it’s an unmet need,” though the company is looking “at a variety of different applications in both research and diagnostics right now,” Naclerio said.He declined to provide details.
The company is “beginning to negotiate our first clinical collaborations” for using SiMoA to identify biomarkers in serum, Naclerio said. He declined to identify the potential partners and the disease areas of interest.
He also declined to specify what iteration the SiMoA technology could take in the future, though he said that it could be eventually commercially marketed as an instrument-and-kit platform.

SiMoA, he said, is not meant to replace ELISAs, which are among the most commonly used techniques for detecting antibodies and antigens. “But for applications where more sensitivity or smaller sample or higher precision is required, we think our technology will be more attractive,” he said. “When you come in with a 100- or a 1,000-time improvement in performance, people will pay attention.”

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