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LC-MS-based Proteomics Enters the Clinic as Integrated Diagnostics Launches Lung Cancer Test

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This story has been updated with comments from outside researchers and clinicians.

LC-MS-based proteomics has officially entered the clinic with the launch this week of Integrated Diagnostics' Xpresys Lung test.

Intended to aid doctors in identifying lung nodules detected via CT scans as likely benign, Xpresys uses multiple-reaction monitoring mass spec to quantify the levels of 11 proteins in patient blood samples.

According to Indi CEO Albert Luderer, the test can rule out an individual patient's lung nodule as being cancerous with a negative predictive value ranging from 84 percent to 98 percent. The test, which Indi is offering out of its CLIA laboratory, is intended for use in patients 40 years or older and with lung nodules ranging from 8 to 30 mm in size.

Beyond its potential usefulness in managing patients at risk of lung cancer, Xpresys is significant as the first multiplexed proteomic test to go to market using MRM-MS on a triple quadrupole instrument. Researchers in the field have for years argued the suitability of such platforms for clinical proteomics, citing their potential for higher multiplexing, lower costs, and improved accuracy. However, a variety of technical challenges including reproducibility, sensitivity, and throughput have traditionally stood in the way (PM 2/11/2011).

Several proteomics-based diagnostics, including Vermillion’s OVA1 and Crescendo Bioscience’s Vectra DA have gone to market in recent years, but these use immunoassay platforms, not mass spec. Biodesix’s VeriStrat lung cancer diagnostic runs on a MALDI-MS platform, but relies on comparisons of broad proteomic profiles rather than mass spec measurements of discrete proteins, as is done in MRM-MS.

Recently, though, a number of groups have made strides toward solving the issues that have kept MRM-MS-based proteomics out of the clinic. For instance, in November 2012, researchers from SISCAPA Assay Technologies and Agilent published on a MRM-MS-based peptide quantitation workflow with a sample cycle time as short as seven seconds (PM 11/16/2012).

In April of this year, a team led by researchers at Thermo Fisher Scientific's BRIMS Center published a paper in Clinical Biochemistry detailing a series of protein quantitation assays developed and run using the company's mass spectrometric immunoassay technology, which links antibody-based protein enrichment to MRM-MS (PM 2/15/2013). Upon publication of that study, BRIMS Center director Mary Lopez told ProteoMonitor that mass spec-based proteomics was "ready for prime time."

The Xpresys launch "demonstrates that mass spec tests are definitely going to get into the clinic," Lopez, who is not affiliated with Indi or the Xpresys test, told ProteoMonitor this week. " In my mind this is a great thing. It's pushing the boundaries. I think it's clear that we're seeing the beginning of a very big wave that's going to be coming in the next few years."

Indeed, while Indi is the first to bring a clinical MRM-MS-based proteomics test to market, companies including Sera Prognostics (PM 3/1/2013) and Applied Proteomics (PM 3/29/2013) have also announced their intentions to do so. The former announced in September that it had appointed Indi co-founder and board member Lee Hood as a scientific advisor.

The Xpresys test uses an Agilent 6490 triple quad instrument linked to standard flow HPLC. The workflow doesn't use any sort of enrichment of its 11 protein targets, but rather uses Sigma-Aldrich's Seppro IgY14 and Human SuperMix protein depletion columns to remove high-abundance proteins, allowing the company to quantify proteins in the low nanogram-per-mL range.

In addition to this high sensitivity, Indi has managed to achieve high reproducibility for its protein measurements. According to Indi President and Chief Science Officer Paul Kearney, coefficients of variation for the majority of the Xpresys test's measurements are less than 5 percent.

In terms of throughput, the company's platform falls somewhat short of the hundreds of samples-per-day capacity envisioned by clinical proteomics pioneers like SAT CEO Leigh Anderson. As currently constituted, Indi's clinical platform can process around 1,000 samples per month using between four and six mass spec instruments, Kearney told ProteoMonitor. Each sample takes roughly 10 days to process, with the majority of that time taken up by sample prep, including an overnight trypsin digestion step. The LC-MS portion of the workflow takes roughly 30 minutes per sample.

The workflow "could be made faster," Kearney said, but, he noted, at this point the throughput offers more than sufficient capacity to meet the expected demand for the test. He cited as a benchmark the example of Genomic Health, which performed around 7,000 Oncotype DX tests during that product's first year on the market.

Lopez likewise noted that while the test's mass spec workflow has its limitations, it nonetheless marks an important step forward for the field.

"Of course you would want to improve parameters," she said. "And you can. There are technologies that can be applied to this to speed things up. But these types of improvements are incremental improvements."

More significant, she suggested, is the launch's demonstration "that the technology has reached a point where it makes it feasible to do this."

Luderer declined to give a specific price for the Xpresys test, but, he told ProteoMonitor, Indi is aiming for pricing similar to Oncotype DX. The Genomic Health test currently lists for around $4,000. The company's mass spec workflow has a high cost per sample, Luderer said – though he declined to provide specifics – but, he noted, "we have a very large margin to play with" given the test's price tag.

The company released the Xpresys test for limited sale to key opinion leaders roughly six weeks ago, hoping to demonstrate the capabilities of the commercial test and gain customers, Luderer said. He did not say if any of these opinion leaders had yet become customers but, he said, "the field feedback is quite clear that we have successfully addressed one of their significant practice dilemmas."

The Xpresys test is intended for analysis of lung nodules picked up via CT scans. Specifically, it is designed to help physicians more confidently rule out lung cancer in patients and put them on a regimen of watchful waiting. Such a test is desirable due to the expense and significant risks of the invasive procedures currently used for determining lung cancer status, like fine needle aspiration and thoracotomies.

The company estimates that the potential US market for the tests is around $2 billion a year. Roughly 3 million lung nodules require evaluation each year, Luderer said, adding that this number will likely go up in light of recent study results suggesting the benefits of increased CT scans in patients at risk of lung cancer.

In 2011, the National Lung Screening Trial – a National Cancer Institute study involving more than 53,000 current and former heavy smokers – released findings that indicated that CT scans reduced lung cancer mortality by 20 percent compared to standard chest X-rays. Given these results, CT scans will likely become a more common procedure moving forward, heightening the need for non-invasive methods – like the Xpresys test – for determining the status of nodules detected via the scans.

Regarding reimbursement for the test, Luderer said Indi has "many covered lives already," though he declined to give a specific number. The company currently has a five-person sales team that it hopes to expand by another six to 10 people in the first half of 2014, he said.

Indi is taking the test to market based on data from multi-site retrospective validation studies testing the panel against nearly 500 patient samples. Two weeks ago it published a study in Science Translational Medicine detailing one of those efforts, a four-site validation study in which they tested this panel against 52 cancer and 52 benign samples (PM 10/18/2013).

The company is also involved in two large prospective validation trials from which it hopes to report initial data in late 2014.

Peter Mazzone, a pulmonologist at Cleveland Clinic who is involved in collecting samples for one of these prospective trials, told ProteoMonitor that the test is promising in that it could provide physicians with additional evidence to support watchful waiting in patients they'd prefer not put through a biopsy.

For instance, he said, he would consider ordering the test in the case of "a patient who is otherwise somewhat ill and may not do well with a biopsy."

On the other hand, "if it's a very health person [in] whom I don't want to miss a cancer regardless of what the blood test tells me, then I probably wouldn't order it," he said.

In total, Mazzone estimated, less than 10 percent of his patients fit the criteria under which he would consider ordering the Xpresys test.

Such a modest figure somewhat undercuts the test's rationale, suggested Howard West, a thoracic oncologist at Seattle's Swedish Cancer Institute. As an oncologist, West is not the target market for the Xpresys test, which is aimed primarily at pulmonologists. However, he said, given his work he is quite interested in questions of lung cancer screening, and, he told ProteoMonitor, he has doubts about the test's ultimate effectiveness in helping patients avoid unnecessary procedures.

"Using it for a cherry-picked situation [like that described by Mazzone] is ok," he said. But, he suggested, such a limited use doesn't substantially address the clinical problem Indi set out to tackle.

And, West said, he fears that the test's low positive predictive value could, in fact, lead to higher numbers of follow-up scans and invasive procedures, rather than fewer.

Although Indi has been quite clear that the Xpresys test is intended only to rule out the possibility of cancer, with indeterminate or positive results not to be taken as indicating that a nodule is cancerous, "the problem is," West said, "that's not the way the world works."

"If you have somebody who has a nodule and the test comes back as anything other than negative, I think it is going to be human nature that the patient or doctors are going to potentially be far more likely to escalate the work-up and now do biopsies when they otherwise wouldn't have, or do scans more frequently than they would have," he said.

Calling Indi and its collaborators "very reputable scientists" and noting that there is a real societal need for a blood test aimed at distinguishing between benign and malignant lung nodules, West said that, nonetheless, the Xpresys test "clearly needs to be validated in a broader setting prospectively to clarify if it leads to less anxiety and fewer unnecessary invasive studies and imaging studies."

Currently, he said, "I have zero confidence that that is actually what would happen in practice."

Mazzone likewise said additional study was needed to determine if the test does, in fact, affect clinical decision making the way Indi expects it will.

"You can speculate that there are a lot of reasons the test could be helpful," he said. However, "how the test ends up being used in the clinic is [currently] unknown."

Several other parties are also working on proteomic tests for determining lung nodule status, including Somalogic, Quest Diagnostics, University of Pittsburgh Cancer Institute researcher William Bigbee, and MD Anderson researcher Samir Hanash (PM 2/23/2012).

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