Novel method could help bring cancer biomarkers to clinic

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 breast cancer cells, 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 mass spectrometry, 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.