Purdue and Indiana universities' proteomics team has been selected as one of five national centers for cancer research. The National Cancer Institute announced last week its selection of the Purdue-IU Analytical Proteomics Team for inclusion in a new consortium to assess proteomic technology and its applications for diagnosis and treatment of cancer. The NCI awarded a $7 million grant to the Purdue-IU team, which pairs Purdue's experts in mass spectrometry and proteomics technology with the expert clinical team of cancer researchers from Indiana University School of Medicine. Together they will focus on technology to diagnose breast and prostate cancer through blood samples. "This is the future of cancer detection in America," said Fred Regnier, Purdue's John H. Law Distinguished Professor of Chemistry and principal investigator for the team. "Proteomics, the study of proteins, holds great promise for more precise diagnosis and tailored cancer therapies through the identification of proteins specific to cancer and other diseases, called 'biomarkers.'" "However, more work needs to be done to establish protocols for these approaches and the technology used. The NCI program creates a consortium for this purpose and is a great advancement for the field. Remarkably, all five centers included breast cancer as an area of study, which will allow for incredible scientific collaboration and evaluation of data from patients nationwide." The consortium will receive $35.5 million in awards and is one of three components of the NCI's $104 million five-year clinical proteomic technologies initiative for cancer national program. "This program is a critical component of NCI's strategy for leveraging the diagnostic and therapeutic potential of proteomics for cancer patients, " said NCI deputy director Anna D. Barker. "I am confident that the complementary proteomic expertise of the awardees, and their commitment to interinstitutional 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." The team, based at Purdue's Bindley Bioscience Center at Discovery Park, will develop protocols and standards for mass spectrometry- based cancer proteomics relating to breast and prostate cancer. The endeavor will involve close cooperation between Purdue and Indiana University experts in proteomics, informatics and cancer biology and treatment. "This is a perfect example of how great things will happen in Indiana when IU, Purdue and the private sector collaborate on life sciences research," said Dr. D. Craig Brater, dean of the IU School of Medicine and vice president of IU with responsibility for life sciences. Four hundred clinical samples will be collected for breast cancer analysis by the Hoosier Oncology Group, an Indiana statewide network of cancer physicians chaired by Christopher Sweeney, an oncologist and associate director of clinical research at the IU Cancer Center. Prostate cancer samples also will be collected from the NCI-sponsored Eastern Cooperative Oncology Group trial. As co-principal investigators, Sweeney and Harikrishna Nakshatri, the Marian J. Morrison Investigator in Breast Cancer Research in the IU Department of Surgery, and others will conduct cancer biology research. Discovery Park's Oncological Sciences Center played a key role in connecting clinical and basic science researchers in the project. The goals of the program are to define existing technologies and identify emerging technologies that will enable precise and reproducible measurement of biomarkers in cancer, said Jiri Adamec, a Purdue research assistant professor and lead scientist at Bindley Bioscience Center and co-principal investigator. Other Purdue team members include research assistant professor Xiang Zhang and chemistry professor Scott McLuckey. The team will employ both electrospray ionization and matrix assisted laser desorption ionization mass spectrometry platforms. "Mass spectrometry-based proteomic approaches have the advantage of excellent sensitivity and high analytical precision," Adamec said. "Our team will focus on the use of this technology in providing insight into breast and prostate cancer biomarkers. These biomarkers will have dramatic impact for cancer diagnostics and therapeutics." The team will use the emerging "bioCD" technology invented at Purdue and commercialized by QuadraSpec, a Purdue Research Park company, to expand the detection and quantification of specific candidate cancer protein biomarkers. The technology enables evaluation of hundreds of proteins of interest from hundreds of samples in minutes by incorporating specific antibodies on a microfabricated optical disk that is read by spinning disc inferometry, said Charles Buck, director of operations for Bindley Bioscience Center. In Bloomington, the startup company Predictive Physiology and Medicine will work with David E. Clemmer, the firm's scientific co- founder and chairman of the IU Department of Chemistry, and Clemmer's team at IU Bloomington to provide ion mobility spectrometry evaluation. This proprietary technology greatly broadens the range for cancer biomarker proteomics studies, Buck said. In Indianapolis, proteomics work will be conducted by the Protein Analysis and Research Center, the academic service component of the Indiana Centers for Applied Protein Sciences (INCAPS), said Mu Wang, director of PARC and an assistant professor of biochemistry and molecular biology at the IU School of Medicine. That work will include planning and execution of the projects to identify and validate targeted biomarkers for breast and prostate cancers. Statistical analysis and processing of the data will be overseen by Jake Chen, assistant professor of informatics at IU and co-principal investigator. "For a large NCI program such as this, data is going to be generated and collected from clinical laboratories, individual research labs at Purdue, Indiana University Purdue University at Indianapolis, IU School of Medicine, IU Bloomington, and various contracting companies across the state," Chen said. "Therefore, it's essential for a team of computational scientists to work together, linking data, storing them, and analyzing them using computational and statistical tools. The work ahead will be very exciting." The team will take advantage of Purdue's discovery pipeline for high- complexity data handling to deal with the challenge of data collection, management, and analysis. This discovery pipeline was developed from cooperation among the Bindley Bioscience, e-Enterprise and Cyber centers at Discovery Park. The NCI's Clinical Proteomic Technology Assessment for Cancer 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. The five teams define a cross-institutional and multidisciplinary network of assessment centers that will 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. CPTAC is one of three major Clinical Proteomic Technologies Initiative program components integrated by the National Institutes of Health 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 have been charged with providing the scientific community with an assessment of current proteomic technologies, developing and assessing novel technologies and computational methods, and creating a central repository of the resources needed to use these proteomic tools.