The field of protein disease marker discovery is gaining momentum, with the initiation of numerous academic and commercial initiatives around the world to study human blood for these biomarkers.
Last week, the Fred Hutchinson Cancer Research Center announced a $4.4 million “Early Detection Initiative,” funded by the Paul G. Allen Foundation for Medical Research in Seattle, the W.M. Keck Foundation of Los Angeles, and Donald Listwin, a California businessman. The program aims at discovering proteins in human serum that indicate cancer at an early stage. Then, this week, Europroteome of Germany said it has started a new collaboration with a number of German academic groups to find protein markers for breast cancer in patient serum samples, and to develop novel tests for early diagnosis. While these projects are already generating data, the Human Proteome Organization is plowing ahead with its plasma proteome project to develop standards for sample collection and to evaluate different analysis technologies.
The initial aim of the FHCRC’s five-year project is to develop and test new methods for detecting proteins in human serum, in collaboration with Ruedi Aebersold’s group at the Institute for Systems Biology. “Eventually, we are hoping to be able to draw blood from people and be able to tell whether they have a certain cancer or whether they have a high predisposition to a certain cancer,” said Heidi Zhang, a staff scientist at the Hutch who is in charge of the sample analysis.
According to Zhang, the center is in the process of acquiring two new instruments that will be dedicated to the initiative: a Micromass LCT ESI-TOF and Thermo’s new LTQ linear ion trap. She and her colleagues will be pursuing a candidate approach, where “we have ideas about what [proteins] could be potentially important,” she said, and will use both LC-MS and LC-MS/MS to identify them. They deliberately decided to “stay away from 2D gels” for fear that gels would not enable them to detect low-abundance proteins. The group will also quantify the samples, using both the ESI-TOF and, to some extent, isotope-coded labeling, she said. Initially, the emphasis will be on method development, paying attention to issues like person-to-person variability between samples. “Once we are comfortable with our approach, we want to apply the same method of analysis to different kinds of cancers,” she said.
Researchers in Ruedi Aebersold’s lab will meanwhile be using an unbiased approach to cancer biomarker discovery in parallel, according to Zhang. Over the next two years or so, the two groups plan to evaluate their methods and validate each other’s results. “At this point, it’s too early to say which approach is going to work out better,” Zhang said. “We believe that both should work for different purposes.”
Aebersold told ProteoMonitor that his group will also help to establish the facility at FHCRC, providing technology and software tools. In addition, his group will be further developing analytical technology, including new methods for serum protein processing and data collection, and develop new software tools to analyze the collected data. “The major challenges relate to the complexity of the serum proteome,” said Aebersold in an e-mail message. “It is huge and largely unknown. There are also important questions how to validate the specificity for a particular disease of potentially detected new markers and, especially, to identify specific markers for early-stage disease.”
According to Martin McIntosh, an FHCRC researcher who is involved in analyzing the data, the initiative will not focus on finding protein patterns, without identifying the proteins. This approach was used by Lance Liotta and Emmanuel Petricoin, researchers at the NCI and FDA, in a Lancet study on ovarian cancer last year. “We think that direction is being explored considerably by people around the country and the world, including a lot of private corporations, and we don’t think that’s where our role should be,” McIntosh said.
At the moment, researchers at the Hutch are performing pilot studies on ovarian and breast cancer serum and tissue samples. Going forward, Zhang anticipates that more principal investigators from the center will join, expanding the project to a variety of cancers. While their ultimate goal is to find protein markers in serum, they will also be studying cell lines, tissues, and other body fluids along the way. Longer term, Zhang hopes the initiative will expand into a larger collaborative effort “on the national and international level,” she said.
Eventually, protein markers that come out of the initiative could be licensed to diagnostic companies, following a model that the FHCRC has already pursued in earlier studies that involved cDNA microarrays. “Our goal is to systematically study the entire process of identifying cancer early,” but not to bring assays to market, McIntosh said.
Meanwhile, Europroteome, a company based in Henningsdorf, Germany, is aiming to do just this. The company is hoping to develop breast cancer protein markers for commercialization, based on a new research collaboration with a German academic consortium called Interdisciplinary Study Group on Gene Environment Interaction and Breast Cancer, or GENICA. According to Christian Knobloch, the company’s vice president for business development, groups in this consortium will be providing Europroteome with several hundred serum samples from breast cancer patients as well as age-matched controls, clinical data, and breast cancer expertise.
Europroteome analyze these samples using “advanced proteomics technologies,” Knobloch said, and will be looking both for single markers and protein patterns, using data mining software developed by Phase-it, a bioinformatics firm Europroteome acquired earlier this year. Knobloch declined to elaborate on the experimental methods, citing that “the area is very competitive.” However, in an earlier study on stomach cancer with the University of Magdeburg, Europroteome used Ciphergen’s SELDI platform, and is considering this as one possible platform for the new project, Knobloch said. The company expects to obtain initial results within six months. These will be published eventually, after Europroteome has filed patents on any markers of interest. It then plans to license these single or multiple markers, or patterns, to a diagnostic company for commercial development. “If it’s a pattern, then we need to be more creative, because today, pattern platforms don’t exist in the market,” Knobloch said.
While serum protein biomarker projects are getting underway, HUPO is still exploring the best ways to analyze plasma proteins, and how to handle sample collection (see PM 1-27-03). McIntosh acknowledged that standards for collecting and processing serum are essential, “especially if in the future we want to combine experiments from different sites.”
In May, HUPO distributed reference samples to 43 laboratories — mostly non-commercial ones — in 14 countries. The labs will use their preferred platforms to identify as many plasma proteins as possible in these as well as their own samples. Initial results of this pilot project will be presented at the upcoming HUPO congress in Montreal in October, and a major workshop to analyze the data is planned for late spring or early summer next year, according to Gilbert Omenn, who heads the project. Final results will be published in a special issue of Proteomics, possibly later next year, and made available through a database that is currently developed by the European Bioinformatics Institute. Longer term, HUPO wants to delve into its own disease-oriented biomarker projects, “in collaboration with many other groups and funding sources,” said Omenn. So far, HUPO has raised more than $500,000 in funding for the pilot project, he said.
— JK