Scientists at the Forsyth Institute, Beth Israel Deaconess Medical Center, and biomarker firm Quanterix announced this week a collaboration to evaluate protein biomarkers for tuberculosis.
The project is funded by a two-year grant for an undisclosed amount awarded to Forsyth by the Bill & Melinda Gates Foundation's Grand Challenges in Global Health program and calls for the researchers to validate seven Mycobacterium tuberculosis proteins that could prove useful in diagnosing the disease.
The grant is one of ten awarded this week under the Grand Challenges program, with several other awards going to proteomics researchers and firms including Somalogic and the Institute for Systems Biology (See story, this issue).
The Forsyth and Beth Israel researchers will use Quanterix's Single Molecule Array, or SiMoA, technology for the validation work. According to Antonio Campos-Neto, the head of Forsyth's Global Infectious Disease Research Center and leader of the effort, the SiMoA system's high sensitivity will hopefully enable detection of the proteins in patient urine samples without the need for sample concentration steps – making for a more clinically useful assay.
Campos-Neto originally identified the proteins using mass spectrometry to analyze urine samples from mice superinfected with tuberculosis. He and his colleagues – including Beth Israel researcher Nira Pollock, one of his partners on the validation project – then repeated that work in humans, identifying tuberculosis proteins in urine samples collected from well-characterized patients provided by a Brazilian collaborator.
The ultimate goal of the research is to develop a protein biomarker-based test that can replace conventional sputum tests, which have poor sensitivity and can require up to six weeks to collect and analyze. Campos-Neto and his team focused on proteins instead of nucleic acids because they thought proteins would enable them to distinguish between latent and active forms of the disease, he said, noting that this is one of the main challenges facing tuberculosis diagnostics.
"Because [PCR-based tests] measure DNA, and very, very minute amounts of DNA, the specificity of such a test is a concern in the sense of it actually correlating with the active disease," Campos-Neto told ProteoMonitor. "If you have a person with basically dead [tuberculosis] in them, that will be a positive test with PCR."
"We hope that, in contrast, by the very nature of proteins' presence in blood and bodily fluids, for a protein to be constantly released, it has to be correlated with the active metabolism of the pathogen," he said. "Therefore, in principle at least, protein detection assays will be correlated with the active [form of the] disease."
Campos-Neto began his discovery work in serum and sputum but shifted to urine because of that medium's simplicity. However, upon moving from the mass spec-based discovery platform to an ELISA format, the researchers found they "had to concentrate the urine because the [immunoassays] were not too sensitive," he said.
"Having to manipulate the urine that much precludes the actual usefulness of the assay in the clinic or at point of care," he noted. "So we started to search for collaborations with groups that had access to or had developed technologies that were more sensitive than conventional ELISAs."
During this search, Campos-Neto came across a paper in Nature Biotechnology by Quanterix researchers in which they used the SiMoA platform to detect prostate-specific antigen in the blood of radical prostatectomy patients at roughly 1,700 times the sensitivity of a typical ELISA (PM 6/11/2011).
"I contacted [Quanterix vice president of research] David Duffy, and he was very interested in doing a collaboration with us," he said. Quanterix is not technically a recipient of the Gates grant, but will be paid by Forsyth for its work on the project as a subcontractor.
The SiMoA platform works essentially like an ELISA, but uses arrays of femtoliter-sized reaction chambers designed to isolate single molecules, enabling each well to serve as an independent assay for a single molecule. According to Quanterix, the platform offers a 1,000-fold improvement over conventional ELISAs, taking immunoassays down into the sub-femtomolar range.
Quanterix has traditionally focused most of its work on using the platform for research into oncology and Alzheimer's biomarkers, but of late the company has ramped up its work on the infectious disease front, recently receiving funding from the US Department of Homeland Security and In-Q-Tel, a non-profit investment firm that delivers technology to the US intelligence community, for research into using the platform for pathogen detection (PM 12/6/2012).
In August, Quanterix CEO Martin Madaus told ProteoMonitor that while protein-based pathogen detection was “a new field of inquiry” for the company, early data had demonstrated the feasibility of using the platform for such a purpose (PM 8/19/2011).
"If you can get the right level of sensitivity, you have a very highly simplified and very elegant way to check for pathogens at very low sensitivity levels," he said, adding that the platform would represent an alternative to PCR-based methods.
Pathogen detection "seems to be a sweet spot for SiMoA," Duffy told ProteoMonitor this week. "You have PCR and other nucleic acid tests that are good at detecting the genes," but not as good at allowing clinicians and researchers to examine the analyte that actually causes the symptoms, "which is usually a protein," he said.
Duffy added that the company was finding that SiMoA offered sensitivity levels comparable to PCR-based tests. "So we have something that could complement or possibly challenge nucleic acid" pathogen detection, he said.
Quanterix plans to commercially launch a research-only version of its SiMoA instrument in 2013 that Duffy said could be useful for infectious disease work in addition to the oncology and Alzheimer's assays that have been the company's focus. However, he acknowledged that for the SiMoA technology to be useful for tuberculosis testing in developing countries – as the Forsyth researchers intend – it would need to be packaged in a portable, point-of-care device.
The company is currently researching such a product, Duffy said, citing a paper in the current edition of Lab on a Chip in which Quanterix and Sony researchers collaborated on a microfluidic chip-based SiMoA device.
"We're already kind of moving in [the direction of a] chip-based, integrated kind of system," he said. "So we think it's definitely possible to develop SiMoA to the point where it could work as a point-of-care, more portable instrument. The arrays and those kinds of microfluidic devices are low cost; the reagents are low cost; so it's definitely possible that we could build a system like that, and that's really what the Gates Foundation is most interested in."
Such a device still remains largely in the concept stage, though, Duffy said. "We're so focused on developing this first [research-only, lab-based] instrument that we haven't had time to work on [a point-of-care device.] However, the work with Sony "has kind of taken us in that direction, so we're thinking about it now so that we'll be ready to start work on that once the [first] system is launched," he added.
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