Novel method could help bring cancer biomarkers to clinic

December 8, 2013

An international team of scientists led by Fred Hutchinson Cancer Research Center cancer proteomics expert Amanda Paulovich, M.D., has demonstrated the feasibility of large-scale, standardized protein measurements, which are necessary for validation of disease biomarkers and drug targets.

The study, to be published Dec. 8 online in the journal Nature Methods, shows that the scientists' targeted protein-detection approach has the potential to systematically and reliably measure the entire human repertoire of proteins, known as the proteome.

The technique, developed by Paulovich, a member of Fred Hutch's Clinical Research Division, and her colleagues, can simultaneously and precisely detect the abundance of hundreds of proteins in many different samples. Researchers from three different groups in Seattle, Boston and South Korea were able to reproduce measurements of 319 proteins from human , showing that the method can be standardized across laboratory and international boundaries.

"This method has the potential to completely revolutionize how we measure human proteins," Paulovich said. "Having a global resource for standardized quantification of all human proteins would set new standards that would undoubtedly increase the reproducibility of preclinical research, which would have a dramatic impact on the translation of novel therapeutics and diagnostics."

Proteins, the molecular workhorses of all biological functions, hold the key to signaling early disease and disease progression. Cancer biomarkers are especially sought after – the protein fingerprints in cells could lead to tests to detect the disease earlier, to identify a person's specific risk of cancer long before it develops, and to better guide patients' treatments. But validating newly discovered biomarker candidates has proven impossible without standardized and reproducible methods to measure their levels, Paulovich said.

Each promising biomarker must be further studied in clinical trials, which requires researchers to measure the abundance of each candidate biomarker in hundreds to thousands of patient samples. Because the odds are extraordinarily low that any one candidate will translate to clinical use, large numbers of proteins must be tested to identify a clinically useful biomarker.

"Right now, you can't make robust measurements of most human proteins," Paulovich said. "More than 10 years after the human genome has been sequenced and we have the full catalog of molecules as important as proteins, we still can't study the human proteome with any kind of throughput in a standardized, quantitative manner."

To address this problem, Paulovich and her colleagues used a sensitive and targeted protein-measurement technology called multiple reaction monitoring , or MRM-MS. This type of mass spectrometry is not new – it has been used for years in clinical laboratories worldwide to measure drug metabolites and small molecules associated with inborn errors of metabolism. More recently, Paulovich and others have begun using it to measure human proteins.

The researchers' method enables highly specific, precise, multiplex (meaning the technique measures several different proteins in a single experimental assay) quantification of a minimum of 170 proteins in 20 clinical samples per instrument per day; no other existing technology has this power.

Because the mass spectrometry technique is targeted, meaning the researchers can tune the instruments to look for a specific subset of proteins in cancer cells or other sample types, it can detect the presence of proteins of interest at much lower levels in tiny blood samples or biopsies than a non-targeted tactic.

"The goal is to position this technology to displace some very old technologies that are currently being used," said Jacob Kennedy, an analytical chemist in Paulovich's group and lead author of the study.

Currently, researchers usually use either Western blotting, ELISA (enzyme-linked immunosorbent assay), or immunohistochemistry (IHC) techniques to measure levels of proteins in clinical samples. These methods are often not reproducible from laboratory to laboratory, rendering validation of candidate biomarkers for clinical use very difficult, and they cannot be used for large numbers of proteins and samples at once.

Paulovich and her colleagues assayed more than 300 proteins known to be produced by breast to validate their technique; their results showed that MRM-MS could recapitulate and extend observations made in previous studies of using other technologies.

The study, which included collaborating research groups from the Broad Institute in Cambridge, Mass., and the Seoul National University and Korea Institute of Science and Technology, South Korea, demonstrated MRM-MS's capacity to measure many proteins at once in a standardized way, laying the foundation for an international, organized effort to quantitate every protein in the human proteome. Their study – the largest to demonstrate the technique's reproducibility across laboratories and the only international study to do so – has pushed the capacity of the technology the farthest, measuring hundreds of pieces where others have measured dozens.

"We really showed what could happen if governments cooperated to build a community resource," she said. "It's doable, it's scalable, and the resource is useful."

Paulovich's team hopes the technique catches on in research communities around the world. To facilitate this, her group is spearheading the development of an open-source website to create a centralized resource of highly validated assays for the research community. The portal, funded by the Clinical Proteomics Tumor Analysis Consortium Initiative (CPTAC) of the National Cancer Institute, is set to launch in early 2014.

Explore further: Predicting ovarian cancer survival through tumor-attacking immune cells

More information: "Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins," Nature Methods, 2013. DOI: 10.1038/nmeth.2763

Related Stories

Predicting ovarian cancer survival through tumor-attacking immune cells

December 4, 2013
One way to predict survival of many types of cancer is by counting the number of tumor-attacking immune cells that have migrated into the tumor in an effort to eradicate it – a sign of the body's immune response to the ...

Early stages of breast cancer could soon be diagnosed from blood samples

November 14, 2013
What could someday be the first blood test for the early detection of breast cancer was shown in preliminary studies to successfully identify the presence of breast cancer cells from serum biomarkers, say the Houston Methodist ...

Mass spectrometry protein assays that match sensitivity of antibody-based clinical tests may speed drug discovery

September 3, 2012
(Phys.org)—Combining two well-established analytic techniques and adding a twist identifies proteins from blood with as much accuracy and sensitivity as the antibody-based tests used clinically, researchers report this ...

New testing strategy detects population-wide vitamin and mineral deficiencies

October 24, 2013
Johns Hopkins researchers have demonstrated that levels of certain proteins in the bloodstream may be used to estimate levels of essential vitamins and minerals without directly testing for each nutritional factor. The team's ...

Recommended for you

A metabolic treatment for pancreatic cancer?

August 15, 2017
Pancreatic cancer is now the third leading cause of cancer mortality. Its incidence is increasing in parallel with the population increase in obesity, and its five-year survival rate still hovers at just 8 to 9 percent. Research ...

Skewing the aim of targeted cancer therapies

August 15, 2017
Headlines, of late, have touted the successes of targeted gene-based cancer therapies, such as immunotherapies, but, unfortunately, also their failures.

Findings pave way for three-drug combination treatment for childhood leukemia

August 15, 2017
UCLA researchers have developed a new approach that could eventually help young people respond better to treatment for acute lymphoblastic leukemia. The scientists discovered in mice that when the production of nucleotides—also ...

Does stronger initial response to cancer treatment predict longer overall survival?

August 15, 2017
It seems like such a simple question: Do patients whose tumors shrink more in response to targeted treatment go on to have better outcomes than patients whose tumors shrink less? Actually, the answer seems simple too. In ...

New study reveals late spread of breast cancer and backs key role of early diagnosis

August 14, 2017
Breast cancer cells that spread to other parts of the body break off and leave the primary tumour at late stages of disease development, scientists from the Wellcome Trust Sanger Institute and their collaborators have found.

Discovery of new prostate cancer biomarkers could improve precision therapy

August 14, 2017
Mayo Clinic researchers have identified a new cause of treatment resistance in prostate cancer. Their discovery also suggests ways to improve prostate cancer therapy. The findings appear in Nature Medicine. In the publication, ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.