A team of researchers has demonstrated that a new method for detecting and quantifying protein biomarkers in body fluids may ultimately make it possible to screen multiple biomarkers in hundreds of patient samples, thus ensuring that only the strongest biomarker candidates will advance down the development pipeline. The researchers have developed a method with the potential to increase accuracy in detecting real cancer biomarkers that is highly reproducible across laboratories and a variety of instruments so that cancer can be caught in its earliest stages.

The results of the Clinical Proteomic Technology Assessment for Cancer (CPTAC) study, which is sponsored by the National Cancer Institute (NCI), part of the National Institutes of Health, and partner organizations, appeared online June 28, 2009, in Nature Biotechnology.

"These findings are significant because they provide a potential solution for eliminating one of the major hurdles in validating protein biomarkers for clinical use. Thousands of cancer biomarkers are discovered every day, but only a handful ever makes it through clinical validation. This is a critical roadblock because biomarkers have the potential to allow doctors to detect cancer in the earliest stages, when treatment provides the greatest chances of survival," said John E. Niederhuber, M.D., NCI director. "The critical limiting factor to date in validating biomarkers for clinical use has been the lack of standardized technologies and methodologies in the biomarker discovery and validation process, and this research may solve that dilemma."

The collaborative and multi-institute nature of this work was critical because many other technologies have yielded test results that vary greatly from one laboratory to the next. NCI’s Clinical Proteomic Technologies for Cancer (CPTC) program was established to help solve this problem. The five institutes that participated in this research as part of the NCI-sponsored CPTAC include the Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Mass.; Vanderbilt-Ingram Cancer Center, Nashville, Tenn.; University of California, San Francisco; Purdue University, West Lafayette, Ind., and Memorial Sloan-Kettering Cancer Center, New York City.

Proteomics studies interactions between proteins, which often work in a tag-team fashion to send important signals within a cell. Most proteomic technologies have been based on mass spectrometry, a decades-old technology that determines which proteins are in a specimen based on the mass and electric charge of fragments of each protein.

The current biomarker discovery process typically identifies hundreds of candidate biomarkers in each study using small numbers of samples, leading to very high rate of invalid biomarkers. The biomarkers that are actually valid — that is, true biomarkers — must be culled from lengthy lists of candidates, a time-consuming and not always accurate process.

MRM provides a rapid way to determine whether a candidate biomarker is detectable in blood. This is critically important for clinical use, as well as in being able to assess whether changes in a candidate biomarker correspond with the presence or stage of a disease. A sophisticated type of mass spectrometry, MRM is designed for obtaining the maximum sensitivity for quantifying target compounds in patient samples.

"Our work demonstrates that this technology has the potential to transform how candidate protein biomarkers are evaluated. SID-MRM-MS, combined with complementary techniques, could provide the critical filter to assess protein candidate performance without the immediate need for other detection or quantification tests. This would provide the critical missing component for a systematic biomarker pipeline that bridges discovery and clinical validation," said senior author Steven Carr, Ph.D., director of the Proteomics Platform at the Broad Institute. "This is an important step forward for the field of proteomics, one that would not have been possible without the collaborative efforts of the CPTAC partners."

In this study, the researchers demonstrated that MRM is highly sensitive and specific, important characteristics that ensure the detection of real disease-specific biomarkers. In addition, using common samples and standardized protocols, they found that MRM is highly reproducible across laboratories and technology platforms. Clinical Proteomic Technologies for Cancer will make common samples and standardized protocols available through its reagents data portal, which can be accessed at http://proteomics.cancer.gov.

This new work grew from a memorandum of understanding between the NCI (through Clinical Proteomic Technologies for Cancer) and the U.S. Food and Drug Administration to accelerate proteomics technology development and application in clinical settings.

CPTAC’s goal is to empower the research community with the tools and methods needed to translate proteomics from laboratory research to clinical utility. These efforts should have implications far beyond cancer, ultimately affecting the diagnosis and treatment of much human disease.

The full listing of participating institutes includes the Broad Institute of the Massachusetts Institute of Technology and Harvard (with the Fred Hutchinson Cancer Research Center, Massachusetts General Hospital, the University of North Carolina at Chapel Hill, the University of Victoria and the Plasma Proteome Institute), Memorial Sloan-Kettering Cancer Center (with the Skirball Institute at New York University), Purdue University (with Monarch Life Sciences, Indiana University, Indiana University-Purdue University Indianapolis and the Hoosier Oncology Group ), University of California, San Francisco (with the Buck Institute for Age Research, Lawrence Berkeley National Laboratory, the University of British Columbia and the University of Texas M.D. Anderson Cancer Center), and Vanderbilt University School of Medicine (with the University of Texas M.D. Anderson Cancer Center, the University of Washington and the University of Arizona).

The Eli and Edythe L. Broad Institute of MIT and Harvard was founded in 2003 to empower this generation of creative scientists to transform medicine with new genome-based knowledge. The Broad Institute seeks to define all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods and data openly to the entire scientific community. Founded by MIT, Harvard and its affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to www.broad.mit.edu.

Memorial Sloan-Kettering Cancer Center is the world’s oldest and largest private institution devoted to prevention, patient care, research, and education in cancer. Their scientists and clinicians generate innovative approaches to better understand, diagnose, and treat cancer. Their specialists are leaders in biomedical research and in translating the latest research to advance the standard of cancer care worldwide. For more information, go to www.mskcc.org.

The Purdue University-Indiana University Analytical Proteomics Team pairs Purdue's experts in mass spectrometry and proteomics technology with the expert clinical team of cancer researchers from Indiana University School of Medicine. The team works to assess proteomic technology and its applications for the diagnosis and treatment of cancer with a focus on technology to diagnose breast and prostate cancer through blood samples. The team is based at Purdue's Bindley Bioscience Center at Discovery Park.

UCSF is a leading university dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care.

NCI leads the National Cancer Program and the NIH effort to dramatically reduce the burden of cancer and improve the lives of cancer patients and their families, through research into prevention and cancer biology, the development of new interventions, and the training and mentoring of new researchers. For more information about cancer, please visit the NCI Web site at http://www.cancer.gov or call NCI's Cancer Information Service at 1-800-4-CANCER (1-800-422-6237).