Skip to main content
Premium Trial:

Request an Annual Quote

Toward Clinical Proteomics


You've got to wonder about scientists who focus on protein biomarkers. While there are plenty of far more stable types of markers, such as DNA, these people have deliberately chosen one of the most finicky analytes out there. As if that weren't enough, they're trying to wrap up multiple proteins into an assay panel and somehow ship them off to a clinical setting.

But these scientists contend that if they can get protein biomarkers to work, their virtues will far outweigh the pains it took to usher them into the clinic. For starters, says Shawn Comella, CEO of Monarch Life Sciences, proteins provide a more direct measure of what's going on in the body than other molecules do. "Just because you have a gene mutation doesn't mean you're going to see a disease," he says. "By measuring the proteins and really correlating it with other data you get a much better picture of what's going on with the patient or with the disease."

Proteins can also be detectable long before other changes — for instance, the DNA changes characteristic of cancer cells — make themselves known, says Drake Zhang at ProtTech. "A protein gives you the best chance for early detection of cancer," he adds, noting that his service company has seen increased demand for work with these kinds of biomarkers.
Early detection is just one goal of identifying and validating protein biomarkers. Potential uses for these kinds of markers include determining drug efficacy, risk stratification, prognosis and diagnosis of patients, classifying patient populations, and toxicology, says Comella.

Current challenges

There's no shortage of hurdles to overcome in the quest to turn protein biomarkers into a clinical mainstay. Perhaps above all else, though, proper validation procedures loom over the field.

The challenge is not about discovering biomarkers, experts say. "Everyone's drowning in candidates," says Emanuel Petricoin at George Mason University. "Every lab has a series of candidate markers that they think are great."

That's in part because proteins are continually changing, so if you're looking for changes in proteins, you won't be disappointed. "I've never seen anybody do a biomarker discovery project that didn't come up with an answer," says Martin McIntosh at the Fred Hutchinson Cancer Research Center. Whether that answer will hold up through validation studies is another issue entirely.

Validation — the step of taking hundreds or thousands of candidate biomarkers and putting them through their paces to find the handful that are really indicative of the disease or condition you're trying to predict or diagnose — is the real trick. "What all of us are lacking is a facile way of validating these multiple markers in a high-throughput system rapidly so that you can really separate the contenders from the pretenders with a large number of samples," Petricoin says.

While the discovery process happens in a massively parallel way, validation is still slowed by the need for high sensitivity and good reagents. "Right now, most people approach biomarker evaluation by generating an antibody [and running] an immunoassay or a radioimmunoassay," Comella says. "It generally takes a long time to generate an antibody, or you can't get a good antibody. It's also expensive."

At Monarch, Comella and his team use a mass spec-based system to eliminate the need for antibodies, but of course that means they're using a platform that is known to be less sensitive than its immunoassay counterpart. "We have some pretty elegant methods of getting around that by depleting proteins, by fractionating or enriching," he says. "Most of the time we can develop an assay that's as sensitive as it needs to be."

Gordon Kapke, senior director of biomarker services at Covance, says that the technology for looking at biomarkers has a way to go before it reaches the necessary point for clinical utility. "Modern LC-MS techniques have appropriate precision and reasonably good sensitivity," he says, "but you still are looking at only a small fraction of the human proteome." He estimates that to look at all of the proteins and truly evaluate their biological relevance "improving the sensitivity of the assays by 10- to 100-fold or more."

Another issue facing clinical proteomics is complexity — something the genomics field is just beginning to iron out itself. Going forward, Petricoin says, it's unlikely that protein biomarker tests will be based on a single analyte; instead, panels of analytes will be studied in concert to diagnose a patient or study drug response. "A lot of people in the last decade have been searching for that elusive single-analyte marker," Petricoin says, using PSA as an example of one that's currently used in the clinic. "The sea change has been toward discovering and measuring multiple markers at once."

Which is, of course, its own can of worms. Investigators have long been familiar with the concept that each protein has its own "sweet spot" of ideal temperature and other conditions. Imagine trying to accommodate a 20-marker panel with 20 different sets of conditions, and you can see what the field is up against. "The platform that you develop to measure those has to be unlike platforms in the past," says Petricoin. "That is not like your father's PSA test."
A final hurdle for all of this work is to have good sample sets to use in validation and other studies. Most biorepositories haven't required sample collection under the conditions necessary to study proteins, Petricoin says — for instance, samples may have sat out for several hours before being stored, rendering them useless to proteomics researchers. McIntosh recommends that scientists try to establish partnerships with clinical collaborators who have access to good samples and whose own work could be furthered with good protein biomarkers.

Life in the clinic

As intimidating as those challenges are, scientists are making progress on all of those fronts, thanks to hard work and funding initiatives from agencies like the National Cancer Institute. Experts say a few key events will help catapult protein biomarkers beyond the research lab.
For starters, Petricoin says that advances in mass spectrometry could go a long way to helping get these biomarkers validated. Hybrid and other novel platforms — including immuno mass spectrometry, multiple reaction monitoring, and the triple quad mass spec — are all progress toward clinical utility, he says.

But scientists have to realize that mass specs will never be a clinician's tool of choice, says Monarch's Comella. Once biomarkers are found and well validated, clinicians will have to be given an easier-to-use assay for them, he says.

Overall, optimism reigns in this field. Comella contends that it'll take just one big success to make the concept truly viable. "The big thing that will probably move it forward is to have a protein biomarker used in a clinical trial," he says. "I don't think we're very far [from that.]"

Power3's Protein Biomarker Play

While everyone else debates the possibilities for protein biomarkers, the folks at Power3 Medical think they've got it worked out. Late last year, the Texas-based company launched a breast cancer test in 12 Middle Eastern countries, where the incidence of breast cancer is three to four times greater than it is in the US. The $500 test consists of a panel of 22 protein biomarkers. Steve Rash, the CEO of Power3, says the company hopes to launch the test in the US as well after it completes an ongoing 100-patient study.

The company is also validating multi-marker tests for Alzheimer's and Parkinson's. "These would be the first known proteomics tests to be commercialized," Rash says. The breast cancer test has demonstrated sensitivity and specificity of 80 percent or more, Power3 says, compared to about 40 percent for the current mammography standard.

Because Power3 performs all of its testing in its own CLIA-certified laboratory, these tests do not require FDA approval, Rash says.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.