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Duplicating their results
July 2009
by David Hutton  |  Email the author
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 WALTHAM, Mass.—Thermo Fisher Scientific announced in June it has reached a collaboration arrangement in which its Biomarker Research Initiatives in Mass Spectrometry (BRIMS) Center will collaborate with NextGen Sciences to apply new technologies to that company's biomarker assay services.

Under the terms of the agreement, the BRIMS Center will work with NextGen to add its latest technologies to the company's BiomarkerExpress platform—a set of biomarker services that rely on a mass spectrometry-based approach called selected reaction monitoring, sometimes called multiple reaction monitoring (SRM)—to assay proteins and peptides in biofluids and tissues.

Under the new agreement, NextGen will have access to the most recent Thermo Scientific mass spec technology, which the company will add to its existing Thermo Scientific-based workflow.

NextGen Sciences CEO Dr. Michael Pisano says his company has been diligent in its search for best-in-class instrumentation.

"While we were putting in place the infrastructure for our biomarker services, it was important that we looked for reliable and accurate instruments, and Thermo Scientific technology was found to be just that," he says. "In concert with our expertise at NextGen Sciences, Thermo Scientific technology delivers the highest quality results to our customers. The combination of Orbitrap technology and triple quad capability enables NextGen Sciences to go from discovery or named proteins to a single or multi-protein assay in a very short timeframe."

Pisano says his company performed proper due diligence in "test driving" and found Thermo Fisher to offer the best instruments to "fit our needs and at the same time better our capabilities."

According to Dr. Mary Lopez, director of the BRIMS Center, the collaboration is a good fit because of what the partners both bring to the table.

"When the BRIMS Center was established in 2004, our focus was on biomarker discovery, and now we are beginning to take that discovery information and translate it into quantitative, targeted assays on our triple-quad platform," she says. "One reason for this approach is that it gives us a high-throughput and very quantitative manner in which to verify and then assay the biomarkers that are discovered."

The result is that researchers can quickly assess whether or not putative biomarkers have any real clinical value. However, Lopez points out that the BRIMS Center is not involved in developing diagnostics.

"We are involved in translating discovery workflows into clinically relevant and robust high-throughput, quantitative assays," she says. "That's where NextGen comes in—because its business model is to develop targeted assays and offer them on a fee-for-service basis to pharma companies or clinical researchers who would like to run multiple assays in a very controlled environment for biomarker verification, clinical trials or therapeutic drug monitoring."

The agreement marks the latest move in a collaboration that has been ongoing for a year. The BRIMS Center and NextGen have also been collaborating on the development of osteoarthritis biomarkers. NextGen is currently testing osteoarthritis biomarker candidates in synovial fluid in 1,000 patient samples provided by Harvard Medical School. Those potential biomarkers were originally discovered through research at Harvard and Case Western Reserve University.

Pisano says he is pleased with the collaboration's ongoing efforts to verify osteoarthritis biomarker candidates in synovial fluid.

"The work is progressing well, and the data are very encouraging," he adds. "The technology offered by Thermo Fisher will continually improve, and as it does, it will improve our abilities."

"For us, it was a very synergistic collaboration," Lopez adds. "We worked with the clinical researchers at Harvard who discovered the osteoarthritis biomarkers and developed the SRM assay on the triple-quad here at BRIMS. Subsequent to that, we transferred the assay protocols to NextGen."

The collaboration also offered the perfect opportunity for the BRIMS Center to determine how well its assays performed with real clinical samples in an environment that was separate from the center.

Lopez says, "NextGen was a perfect partner for demonstrating inter-lab reproducibility of the assay. This was immediately tested by the Harvard clinical researchers who needed to run large numbers of samples to see if their putative biomarkers could segregate disease from normal samples in a large, blinded cohort."

Lopez also notes that NextGen is carrying out advanced work on the development of assays targeting other protein biomarker candidates in CSF, plasma and tissue.

"The company has the infrastructure and expertise necessary to develop and apply peptide assays in a commercial CRO setting," Lopez said. "Above all, NextGen Sciences has a track record for delivering the highest quality data to the client, meeting short deadlines and providing excellent support through all stages of its research projects."

Historically, immunoassays have been the gold standard for monitoring levels of protein biomarkers in samples. While these assays can provide high quality data, the development of multiplexed, quantitative protein assays has been a bottleneck in clinical research.

NextGen is addressing this bottleneck by developing protein and peptide biomarker assays using mass spectrometry-based SRM. SRM has been used for more than 20 years to monitor small molecule concentrations. In peptide SRM, proteotypic (unique) peptides from protein biomarker candidates are monitored. Availability of reproducible assays has been a major barrier for biomarker research and development.

According to Pisano, the biomarker assay development pipeline at NextGen Sciences is iterative and can handle large numbers of proteins, permitting investigators to empirically validate and select all of their biomarkers.

Utilizing Thermo Fisher's new mass spectrometry technology and software can boost NextGen Sciences' efforts and capabilities with regards to BiomarkerExpress.

"It adds the latest line of instrumentation and software that enables NextGen Sciences to remain at the cutting edge, giving us the ability to offer best-in-class services," notes Pisano.

As the collaboration unfolds, Lopez points out that the results have been very encouraging since the tests run at BRIMS and NextGen are consistent in demonstrating that Thermo Fisher's technology platform for SRM assays delivers a high degree of reproducibility across different sites.

"NextGen will eventually offer this test on a fee-for-service basis to other researchers," she notes. "That shows that we have successfully been able to take putative biomarkers, translate them into a quantitative SRM-based assay and then, through a CRO partner, offer the assays to researchers who would like to test their clinical samples."

The ultimate measure of success is that the BRIMS Center has been able to develop the workflow, translate it to another lab and demonstrate that it is robust and reproducible and that the results are reliable, she says.

"Over the past few years, several research teams and academic consortia have been trying to accomplish site-to-site reproducibility of SRM assays and to date, I think the results have not been very encouraging," concludes Lopez. "It is one of the big challenges in proteomics and I believe that in this focused collaboration, we have been able to achieve some measure of success."
 
 
Code: E070919

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