The National Cancer Institute last week announced that a team co-led by Fred Hutchinson Cancer Research Center and the Broad Institute in Cambridge, Mass., has been selected to participate in the Clinical Proteomic Tumor Analysis Consortium, or CPTAC.
The researchers will aim to identify and analyze proteins in the blood that are associated with genetic alterations that lead to cancer. The overarching goal of CPTAC is to improve the ability to prevent, diagnose and treat cancer.
The team will receive approximately $9 million in federal funding over three years with the possibility of an additional two years of funding pending scientific review mid-program.
Paulovich co-leads collaboration
Co-principal investigators of the Hutchinson Center-Broad team are Dr. Amanda Paulovich, of the Hutchinson Center’s Clinical Research Division, and Dr. Steven Carr, director of proteomics at the Broad Institute of MIT and Harvard. Their group is among five NCI-funded Proteome Characterization Centers nationwide that will work to define the interplay of genes and proteins on cancer development and prognosis.
This is not the first time the Paulovich and Carr laboratories have collaborated. In 2006 they, along with Dr. Leigh Anderson, founder and CEO of the Plasma Proteome Institute in Washington, D.C., were selected to co-lead one of five teams that received NCI funding during the first phase of the consortium, which was launched with the goal of improving success rates for developing new blood tests for cancer.
Understanding the body’s protein landscape is important because proteins are the workhorses of the cell that carry out genetic instructions. Changes in the structure or abundance of proteins are associated with genetic mutations that cause diseases such as cancer.
End goal: blood tests for cancer
Ultimately, the “holy grail” of proteomics – the large-scale study of proteins – is the discovery of protein biomarkers that could be used to create reliable and inexpensive blood tests to identify the onset and risk of a wide range of cancers and other diseases so they could be prevented or treated at the earliest possible stage, when cure rates are highest.
For the project, Paulovich, Carr and colleagues will continue their work, which harnesses a highly sensitive and targeted analytical technology – multiple reaction monitoring mass spectrometry – to develop assays, or tests, to measure levels of proteins found in cancer cells and patient blood. Unlike traditional mass spectrometry, which attempts to detect all proteins in a biological sample in a scattershot fashion, this technology is highly targeted, allowing researchers to calibrate the equipment to specifically look for peptides, or protein fragments, of interest, filtering out the rest as white noise.
Success with targeted mass spectrometry
Papers detailing the use of these technologies were published back-to-back by the Paulovich and Carr laboratories in the June 2011 issue of Nature Biotechnology.
During the second phase of consortium funding, Paulovich, Carr and colleagues throughout the network will use data and biospecimens from The Cancer Genome Atlas, or TCGA, a collaborative effort by NCI and the National Human Genome Research Institute. The CPTAC network will use proteomics to analyze cancer tissues that have also been characterized at the gene level by TCGA. The genomic and proteomic data will be combined to study the biology of the tumors, as well as to identify potential new diagnostic tests for cancer.
The other Proteome Characterization Centers are based at Pacific Northwest National Laboratory in Richland, Wash.; the University of North Carolina in Chapel Hill and Boise State University in Idaho; Johns Hopkins University in Baltimore; and Vanderbilt University in Nashville.