The IU and Purdue Analytical Proteomics Team was awarded a grant of about $7 million as one of five national centers selected by the NCI for its clinical proteomic technologies initiative for cancer, a five-year, $104 million national program. The five grants, totaling $35.5 million, will establish a collaborative network to assess the proteomics technologies used to improve cancer research and treatment.
Proteomics is the study of proteins: their structure, function and how they interact with each other. The goal of the NCI initiative is to enable cancer researchers to make use of standardized proteomics methodologies to discover proteins and protein components -- biomarkers -- that are relevant to cancer.
Indiana is well known for having experts in proteomics at Purdue, IU-Bloomington and the IU School of Medicine in Indianapolis, as well as private industry. The Analytical Proteomics Team grant will pair those proteomics experts with cancer researchers and clinicians at the IU School of Medicine and experts in statistical and computer analysis at IU's School of Informatics.
Fred Regnier, Ph.D., Purdue's John H. Law Distinguished Professor of Chemistry, will be principal investigator for the team.
"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 D. Craig Brater, M.D., vice president of IU with responsibility for life sciences and dean of the IU School of Medicine.
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, MBBS, 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, Ph.D., Marian J. Morrison Investigator in Breast Cancer Research in the IU Department of Surgery, and others including Bryan Schneider, M.D., assistant professor of medicine, will conduct cancer biology research.
The IU and Purdue proteomics scientists will employ a variety of mass spectrometry techniques in the project. The start-up company Predictive Physiology and Medicine will work with David E. Clemmer, Ph.D., the firm's scientific co-founder and former chairman of the IU Department of Chemistry, and Clemmer's team at IU Bloomington to provide ion mobility spectrometry evaluation. This proprietary technology adds several orders of magnitude increased dynamic range for cancer biomarker proteomics studies.
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, Ph.D., 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. Informatics work will be overseen by Jake Chen, Ph.D., assistant professor of informatics at IU and co-principal investigator, working with a team of informatics specialists from IU Bloomington and biostatistics experts at the IU School of Medicine.
"For a large NCI program such as this, data is going to be generated and collected from clinical laboratories, individual research labs at Purdue, IUPUI, IU School of Medicine, IU Bloomington, and various contracting companies across the state. 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," Chen said.
The team will take advantage of Purdue's Discovery Pipeline for high complexity data handling to deal with the challenge of data collection, management, analysis and mining of the high throughput proteomics approaches. This discovery pipeline was developed from cooperation between the Bindley Bioscience, e-Enterprise, and Cyber centers at Purdue's Discovery Park.