Feature
Partnering on Proteomics
December 21, 2006
IU–Purdue team researches early cancer detection with funding from the National Cancer Institute
Imagine that in the not-too-distant future, a patient visits the doctor for a routine physical and has blood drawn. The results show one problem: protein “biomarkers” for pancreatic cancer are detected in the blood sample. The good news is the cancer is diagnosed very early. With immediate, aggressive treatment, the patient has a good chance of being cured.
The patient likely will thank the doctor, but he probably won't know to thank the science that helped make the cure possible: proteomics—the study of the universe of proteins (the proteome)—that make up the structure and carry out the operations of all the cells in our bodies.
Indiana is well known as a center of excellence in proteomics, with experts in the field at IU Bloomington, at Purdue in West Lafayette, and in Indianapolis. That statewide expertise helped a team of Indiana researchers from Purdue and IU land a $7 million grant from the National Cancer Institute (NCI) in August, just one of five such grants awarded nationally to develop better tools for discovering biomarkers for cancer.
Scientists already know that proteins have the potential to be used as cancer detectors. What proteomics experts don’t know is how best to make this happen. Despite the reams of data generated in individual labs, proteomics experts still have only a sketchy sense of what their tools are capable of doing and which work best.
“What’s been happening for the past few years, which is typical in new fields, is that proteomics researchers in various universities get grants and do research without thinking much about how similar research is being done in other places,” said Fred Regnier, a professor of chemistry at Purdue University and one of the world’s foremost analytical chemists working on proteomics. “And the problem is that because there are no standards for technology, research methods, or even terminology, it’s next to impossible to move beyond the experimental stage.”
Now, thanks to the NCI grant, the joint Purdue-IU analytical proteomics group has a chance to help bring order to the chaos. As principal investigator, Regnier has assembled a crack team including Purdue analytical chemists, clinical cancer specialists at the IU School of Medicine, and biomedical information experts at the IU School of Informatics. The collaboration also includes scientists at the Bloomington-based start-up company Predictive Physiology and Medicine and the Indiana Centers for Applied Protein Sciences (INCAPS) in Indianapolis. Their mission is to help set proteomics on the right path by determining which technologies work best to enlist proteins in the battle against cancer.
“Assembling the team was easy; we have some of the world’s top analytical chemists, protein analysts, cancer researchers, and bioinformatics experts in Indiana,” Regnier said. “Now comes the hard part—figuring out how to best work together to move proteomics beyond the lab to clinics where we can use it to actually help people fight cancer.”
In one sense, the solution to the proteomics problem is straightforward: collect lots of blood samples containing similar proteins, analyze them using several different technologies, then crunch the data to determine which machines are best at analyzing protein samples and making them useful cancer detectors. And that, in a nutshell, is what the Purdue-IU team will do.
The team’s first step is to collect blood samples from patients with breast cancer—a task assigned to the Hoosier Oncology Group, a statewide network of cancer physicians and researchers.
“It may sound straightforward, but it’s a fairly delicate job,” said Christopher Sweeney, chair of the Hoosier Oncology Group and associate director of clinical research at the IU Cancer Center. “First, we have to get samples from patients with clinical features and related proteins that match the features we’re looking for. Then we have to freeze and store the samples without damaging them.”
Sweeney compares working as part of an interdisciplinary team to participating on a relay team. “If you’re running a 400-meter race and have only part of the team, you can only go a quarter of the way,” he said. “But if the team is working together, you hand off the baton and go all the way. The oncology team’s goal is to do our job and then hand off the next portion of the project.”
The next step actually involves two handoffs: one to David Clemmer, holder of the Robert and Marjorie Mann Chair in Chemistry at IU Bloomington and co-founder of Predictive Physiology and Medicine (PPM), a company based in Bloomington, and another to INCAPS in Indianapolis. Both companies will test, among other technologies, an emerging protein analysis technology called “bioCD,” invented at Purdue and commercialized by QuadraSpec, a Purdue Research Park company. PPM and INCAPS scientists will test the technologies’ ability to analyze hundreds of proteins and identify the ones best suited to act as biomarkers for breast cancer.
“It’s important to understand that we’re not looking to discover new biomarkers for cancer,” said Mu Wang, director of INCAPS’ Protein Analysis and Research Center. “We’re focused on testing the equipment and doing technology comparison, which is crucial. While we’re testing one platform, people in Bloomington and at Purdue will be testing other methods. The technology has evolved so rapidly over the past five years that, as the NCI has realized, we really need to go back to the beginning and evaluate what we’ve got.”
The NCI’s hope is that alongside the work of other collaborative efforts across the country, the Purdue-IU team’s rigorous testing of proteomics technology will create a clearer picture of which techniques will ultimately work best in a clinical setting. That won’t happen, though, without the statistical analysis and data processing prowess of IU bioinformatics expert Jake Chen.
“The massive amounts of data generated by the teams at IU, Purdue, and PPM won’t be worth much unless there’s a computing infrastructure in place to bring all that information together, organize and analyze it, and make the data available to everyone on the project,” said Chen. “It’s a daunting, but exciting, challenge.”
From his perspective as the team’s principal investigator, Regnier is optimistic about the new direction in NCI-funded proteomics research. Another term for what the NCI and the Purdue-IU team is after, Regnier explains, is “transitional medicine”—the transformation of basic research findings into diagnostic technologies, medicines, cures, and other commercial products.
“It’s not by accident that I’ve involved PPM and INCAPS in this project,” Regnier said. “They’re companies that know how to turn ideas and research into products. And, ultimately, that’s what we’re after. Indiana has a powerful force in analytical chemistry and proteomics. Now we need to work together to turn our potential into companies, jobs, and products that will better all of our lives.”
