Researchers at the University of Virginia have received a five-year, $1.5 million grant from the National Cancer Institute to develop a proteomic platform that will reduce the time and effort needed to quantify proteins, which in turn could hasten the discovery of cancer biomarkers.
The award was one of 15 given recently by the NCI’s Clinical Proteomic Technologies Initiative for Cancer under a component called the Advanced Proteomic Platforms and Computational Sciences and addresses a technique that is becoming increasingly important as proteomics progresses from the mere identification of proteins and peptides to a more quantitative approach.
UVA researchers are basing their work on a platform they call PICquant, also the name of the software on which the platform is based.
Dennis Templeton, the lead investigator on UVa’s project, said that quantifying proteins by mass spectrometry is currently a laborious task that, depending on the number of individual spectra, can take months to quantify by hand. Templeton is also the chairman of the department of pathology at the UVa School of Medicine.
With the PICquant software, however, Templeton and has colleagues are able to use label analysis to find out “what the mass of the unmodified peptide is, what the charge of the peptide is, and what the quantitation [is] between the heavily labeled and the lightly labeled molecule, all in an automated way.”
The approach, he said, “allows dozens of samples to be analyzed in the time it takes to label and quantify one manually.”
Part of the APPCS award will go towards modifying the PICquant platform so it can be used by researchers outside of Templeton’s group. Right now, proprietary file formats used by Thermo are the main barrier to broader dissemination of the method, Templeton said. Working around those formats is not “a trivial thing,” he said, but noted that his group may have found solutions to the problem.
“[Thermo] makes it hard, but we can break that open,” he said. “There are ways of taking [Thermo] files and turning them into open-type data formats. MzXML is one and we are using that already. And we can probably get mzXML files from other platforms to input into the PICquant software. It’s just that we haven’t tried it yet.”
Another obstacle is that the UVa group tweaked its mass spec in order to get the data it needed. Depending on the instruments used by other researchers, that could be a difficult step, Templeton said.
Once the PICquant platform is fully set up, Templeton and his colleagues hope to further their work developing urine-based, biomarker diagnostics for breast, uterine, and ovarian cancers. The group chose urine as the basis for its test because of the availability of it.
“Urine is, next to spit, the easiest biological sample to get,” Templeton said. He also said that every metabolic process in the body ends up leaving protein traces in urine, making urine an excellent source for protein screening.
While many other researchers have chosen blood as the basis for their biomarker discovery work, Templeton said blood is a less stable biological sample. “What’s in blood now won’t be the same in 10 minutes in a tube.”
The total protein content in urine is also much lower than in blood, making it easier to identify low-abundance proteins, Templeton said.
“The major problem with proteomics, for mass spectrometry at least, is that you have an incredibly wide range in protein concentrations,” he said. “You have a total amount of protein that’s high, but almost all of the protein in serum is [made up of] two or three proteins. So if you’re looking for something that’s the hundredth-most-abundant protein, it’s very hard to see that in blood because the albumin gets in the way.”
As a result of the ACCPS award and the further development of PICquant, Templeton said that in five years his group should be able to identify about a dozen proteins found in the urine of cancer patients but not in the urine of healthy ones. They should also have begun work on developing of antibodies for them, he added.
CPTI, a five-year, $104 million program, was created a year ago by the NCI to evaluate the use of proteomic tools and data resources for cancer research and to encourage greater use of proteomic technologies and methods to find possible cures for cancer.
The APPCS awards announced in late September total $56 million to be dispersed over five years. Winners of the awards are conducting research on topics ranging from developing more reliable statistical algorithms and models for analyzing large proteomic data sets to developing platforms for screening serum for cancer membrane proteins.
In addition to the APPCS awards, NCI last month announced the five winners of CPTI’s Clinical Proteomic Technology Assessment for Cancer awards. Those winners will share $35.5 million over five years to evaluate and test proteomic technologies applicable for cancer research [See PM 09/28/06].