Center team chosen for collaborative proteomics network

The National Cancer Institute recently announced funding for a major component of its $104 million, five-year Clinical Proteomic Technologies Initiative for Cancer (CPTI). Awards totaling $35.5 million over five years will establish a collaborative network of five Clinical Proteomic Technology Assessment for Cancer (CPTAC) teams. Each of these teams will bring complementary expertise to assess the full spectrum of measurement technologies for proteins and peptides relevant to clinical cancer research and practice.

The Hutchinson Center will be major contributor to the network, working on a team led by the Broad Institute of MIT and Harvard University. The Clinical Research Division laboratory of Dr. Amanda Paulovich, will serve as the team's mass-spectrometry performance site. Drs. Peggy Porter, Human Biology Division, and Connie Lehman, Seattle Cancer Care Alliance, will provide breast-cancer clinical samples for the entire consortium; and Pei Wang, Public Health Sciences Division, will provide data analysis. Other collaborating institutions on the team include the Plasma Proteome Institute and the University of Victoria.

CPTAC teams will guide and provide resources to the broader cancer-research community. The network's collaborative efforts will enable researchers conducting cancer-related protein research at different laboratories to use proteomic technologies and methodologies to directly compare and analyze their work. In current cancer proteomic research, standardized technologies and methodologies are critically needed to more effectively discover and validate proteins and peptides relevant to cancer, or biomarkers. This should lead in turn to improved diagnostics, therapies and even prevention.

"With this far-sighted program, NCI is taking on one of the most challenging tasks facing researchers in the proteomics field," said Dr. Lee Hartwell, Center president and director. "This effort is absolutely essential if we are to accelerate the advancement of proteomics into clinical practice."

CPTAC research teams

CPTAC awardees were chosen based, in part, on the broad expertise of their proteomic-research teams and their familiarity with and regular use of a wide range of proteomic technologies. These five CPTAC teams define a cross-institutional and multidisciplinary network of assessment centers that will rigorously evaluate and compare different commercially available proteomic platforms and analysis-software packages in the context of their potential applicability to cancer. They will also work together to develop a comprehensive approach to assess intra-platform and inter-laboratory variability in these measurement technologies. The awardees include: Broad Institute of MIT and Harvard; University of California, San Francisco/Lawrence Berkley National Laboratory; Vanderbilt University School of Medicine; Purdue University; and Memorial Sloan-Kettering Cancer Center.

"This program is a critical component of NCI's strategy for leveraging the diagnostic and therapeutic potential of proteomics for cancer patients," said Dr. Anna Barker, NCI deputy director. "I am confident that the complementary proteomic expertise of the awardees, and their commitment to inter-institutional collaboration and real-time data sharing, will enable the development of biomarkers to contribute to a new generation of molecularly based interventions to diagnose, treat and prevent cancer."

Specific objectives of the CPTAC program teams include:

• evaluating the performance of proteomic-technology platforms and standardizing approaches to developing applications of these platforms,
• assessing proteomic platforms for their ability to analyze cancer-relevant proteomic changes in human clinical specimens,
• establishing systematic ways to standardize proteomic protocols and data analysis among different laboratories,
• developing and implementing uniform algorithms for sharing bioinformatics and proteomic data and analytical/data mining tools, and
• developing well-characterized material and bioinformatics resources for the entire cancer research community.

The promise of proteomics

CPTAC is one of three major CPTI program components — including Advanced Proteomic Platforms and Computational Sciences and the Clinical Proteomic Reagents Resource — developed over the past two years with input from the research community. The components are integrated efforts by NCI to address the fundamental scientific requirements that must be met in order to realize the promise of proteomics for cancer diagnosis and therapy. Together they will provide the entire scientific community with a rigorous assessment of current proteomic technologies, the development and assessment of novel technologies and computational methods, and a central repository of the resources needed to productively use these proteomic tools.