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Quanterix Believes its Single Molecule Array Tech Has a Molecular Dx Future

Fueled by a recent $15 million venture capital investment, Cambridge, Mass.-based Quanterix said it will now begin the first of what it hopes will be many clinical partnerships that use its flagship single-molecule array platform.
The financing, announced last month, was the second and final tranche of a Series A round co-led by ARCH Venture Partners, Bain Capital Ventures, and Flagship Ventures. The first tranche, which closed in June 2007, was for $4 million, while the second was worth $11 million.
Quanterix was founded last year by Tufts University chemistry professor David Walt and former ParAllele Bioscience CEO Nicholas Naclerio. The company has an exclusive license to a broad intellectual property portfolio developed by the Walt lab at Tufts.
Naclerio, who previously served as general manager of Motorola’s life-science business, told BioArray News last week that Quanterix’s single molecule array, or SiMoA, platform is well suited for molecular diagnostics applications, and that the company is already engaged in its “first clinical collaborations” with undisclosed partners.
He said that Quanterix will spend the Series A money to begin to develop products. “The first phase of the company is proving the science,” he said. “The second phase is to develop working prototypes and turn it into a product. We will take clinical work with various collaborators to show what you can do when you have that kind of technology.”
Quanterix’s SiMoA technology comprises arrays of femtoliter-sized reaction vessels, each vessel sized to confine a single molecule of interest. The arrays are formed by etching tens to hundreds of thousands of separate reaction vessels into the end of an optical fiber bundle.
Each vessel can be used to trap single molecules, and the optical fiber bundle carries light into and out of each vessel, allowing each well to function as an independent assay for a single molecule. Quanterix’s system also features a proprietary image-capture device and image-analysis software.
“We use the word array in our platform, but it is not really an array in the sense of an Affy or an Agilent or an Illumina array,” Naclerio said. “In those cases, an array is used to do multiplex analysis, looking at lots of analytes simultaneously. In the case of Quanterix, the multiplexing is looking at single molecule events at the same time.”
“If you are looking at binding kinetics, you are looking at a series of events where molecules interact and creating an aggregate value,” Naclerio said. “We determine these values by looking at one molecule at a time, not an ensemble.”
Quanterix’s first application is designed to measure the concentration of specific proteins in a complex mixture like serum or blood. The company believes SiMoA could potentially be used to detect infectious pathogens without the need for culturing or other amplification steps.
Naclerio said this use could be used to test blood, or for food safety and biosecurity applications. He also said they can be used in both research and diagnostics “where precision and specificity means you can detect cancer earlier, an infection earlier, or detect a protein biomarker in a part of the body where you wouldn’t normally find it,” such as serum versus spinal fluid, or urine versus tissue. “We expect that that will translate into more valuable diagnostic tests,” Naclerio said.
“Imagine taking a serum sample and instead of in a test tube adding some reagent that changes color in the presence of PSA molecules, and looking at a test tube and seeing [whether] is it clear or red or dark red, we take that sample and divide it up into tens of thousands of reaction volumes.

“This is not some esoteric technology that only a few research centers will have.”

“In each one of those volumes, we carry out a reaction [whose results are either] positive or negative – is there a molecule present in that reactor or not?” he said. “On average there will be zero or one molecule present in each well. We are making digital measurements by looking well by well, and counting the molecules we see.”
Once ready for market, Quanterix’s protein concentration-measurement application will most likely compete against existing technologies like enzyme-linked immunosorbent assays, which represent the most common way to measure proteins in complex mixtures.
“That is the technology that we would be most likely replacing for that particular application, as we would come in and have assays that have substantially more sensitivity,” he said.
ELISAs, though, are typically performed in microtiter plates, which are less expensive than most array platforms on the market. Naclerio declined to discuss pricing for the platform, but said that the company aims to sell the platform at a competitive price.
“This is not some esoteric technology that only a few research centers will have,” Naclerio said. “Our goal is to develop this to the point where it’s affordable for life-science researchers, as well as affordable for use in clinical diagnostics.”
Keith Crandell, co-founder and managing director of ARCH Venture Partners, recently told BioArray News’ sister publication Biotech Transfer Week that there are currently a few hundred diagnostic tests that use ELISA to identify protein biomarkers of interest, but that research has shown that at least another 1,000 protein biomarkers exist that are below ELISA’s detection limit.
“The opportunity is to develop a reliable, low-cost, reproducible test with high specificity for these biomarkers, and that is what Quanterix is pointed toward,” said Crandell, who is also a Quanterix director. “The brilliance in the technology is how simple it is. That allows it to be highly reproducible and low-cost.
“If you are going to push out the technology to the broadest possible group, you have to be able to deliver it consistently, and it can’t cost a lot,” he added (see BTW 9/3/2008).
In addition to protein-concentration measurement, Quanterix hopes to market SiMoA as a tool for measuring kinetic binding. Because it can interrogate hundreds to thousands of individual enzyme molecules, and therefore allow the distribution of individual kinetic trajectories to be determined and compared to bulk enzyme experiments, SiMoA can measure and obtain binding constants from the statistics of many single molecule measurements in a single experiment, according to Quanterix.
According to Naclerio, measuring the range of interactions between individual enzymes and a drug candidate could potentially provide clinicians with a tool to design specific interactions for sub-populations of enzymes, for example. 
Time to Build
Discussing the company’s future plans, Crandell speculated that Quanterix could go the way of ParAllele or True Materials, should its technology platform prove attractive to some of the larger companies in the field.
“I’m sure Illumina and many of the other leading companies in diagnostics will be interested in this as it matures,” Crandell said. “Usually [you need] a small focused entrepreneurial group to take that risk to sort of drive it forward. That’s the stage we’re at.
“This was one of those deals that comes along every five years or so, and you have to jump on it, because you’re working with such a good group of people and the technology is so promising,” he added.
However, Naclerio said that his immediate goal is to “build a successful company and to maximize the return for our investors,” whatever the path. “Right now we need to develop a basic platform and to collaborate with clinicians that have interesting applications,” he said. “We are always open to, and will always evaluate, various partnership opportunities as they come along.”

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